diff --git a/doc/if.html b/doc/if.html index b89b1d69d3..1821b9088c 100644 --- a/doc/if.html +++ b/doc/if.html @@ -38,7 +38,7 @@ if "${eng} > ${eng_previous}" then "jump file1" else "jump file2"

Description:

-

This command provides an in-then-else capability within an input +

This command provides an if-then-else capability within an input script. A Boolean expression is evaluted and the result is TRUE or FALSE. Note that as in the examples above, the expression can contain variables, as defined by the variable command, which @@ -51,7 +51,7 @@ commands (t1, t2, ..., tN) are executed. If it is FALSE, then Boolean expressions associated with successive elif keywords are evaluated until one is found to be true, in which case its commands (f1, f2, ..., fN) are executed. If no Boolean expression is TRUE, then the -commands associated witht the else keyword, namely (e1, e2, ..., eN), +commands associated with the else keyword, namely (e1, e2, ..., eN), are executed. The elif and else keywords and their associated commands are optional. If they aren't specified and the initial Boolean expression is FALSE, then no commands are executed. diff --git a/doc/if.txt b/doc/if.txt index 4bc396b2a7..bbbb85e05b 100644 --- a/doc/if.txt +++ b/doc/if.txt @@ -35,7 +35,7 @@ if "$\{eng\} > $\{eng_previous\}" then "jump file1" else "jump file2" :pre [Description:] -This command provides an in-then-else capability within an input +This command provides an if-then-else capability within an input script. A Boolean expression is evaluted and the result is TRUE or FALSE. Note that as in the examples above, the expression can contain variables, as defined by the "variable"_variable.html command, which @@ -48,7 +48,7 @@ commands (t1, t2, ..., tN) are executed. If it is FALSE, then Boolean expressions associated with successive elif keywords are evaluated until one is found to be true, in which case its commands (f1, f2, ..., fN) are executed. If no Boolean expression is TRUE, then the -commands associated witht the else keyword, namely (e1, e2, ..., eN), +commands associated with the else keyword, namely (e1, e2, ..., eN), are executed. The elif and else keywords and their associated commands are optional. If they aren't specified and the initial Boolean expression is FALSE, then no commands are executed. diff --git a/tools/moltemplate/LICENSE.TXT b/tools/moltemplate/LICENSE.TXT new file mode 100644 index 0000000000..c8c1ec0819 --- /dev/null +++ b/tools/moltemplate/LICENSE.TXT @@ -0,0 +1,28 @@ + +Author: Andrew Jewett, Shea Group, http://www.chem.ucsb.edu/~sheagroup/ +Copyright (c) 2013, Regents of the University of California +All rights reserved. +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + * Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + * Neither the name of the University of California, Santa Barbara nor the + names of its contributors may be used to endorse or promote products + derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE +LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF +THE POSSIBILITY OF SUCH DAMAGE. + diff --git a/tools/moltemplate/README.TXT b/tools/moltemplate/README.TXT new file mode 100644 index 0000000000..2e73b63744 --- /dev/null +++ b/tools/moltemplate/README.TXT @@ -0,0 +1,61 @@ + -- Description: -- + +Moltemplate is a cross-platform text-based molecule builder for LAMMPS. + + -- Typical usage: -- + +moltemplate.sh [-atomstyle style] [-pdb/-xyz coord_file] file.lt + + -- Web page: -- + +Documentation, examples, and supporting code can be downloaded at: + + http://www.moltemplate.org +The most up-to-date version of moltemplate can be downloaded here. +(After download, you can unpack the archive using: + tar xzf moltemplate_2012-3-31.tar.gz +The date will vary from version to version.) + +---------------------------------------------------- +---------- INSTALLATION INSTRUCTIONS: ------------ +---------------------------------------------------- + +This directory should contain two folders: + src/ <-- location of all python and bash scripts + common/ <-- location of shared force fields and molecules + +The ``moltemplate.sh'' script and the python scripts that it invokes are +located in the ``src/'' subdirectory. You should update your PATH environment +variable to include this directory. + +If you do not know what a PATH environment variable is, read: + http://www.linfo.org/path_env_var.html +(I receive this question often.) + +It is also a good idea to set your MOLTEMPLATE_PATH environment variable to +point to the ``common/'' subdirectory. +(Force fields and commonly used molecules will eventually be located here.) + + -- Installation example --- + +Suppose the directory with this README.TXT file is located at ~/moltemplate. + +If you use the bash shell, typically you would edit your +~/.profile, ~/.bash_profile or ~/.bashrc files to contain the following lines: + export PATH="$PATH:$HOME/moltemplate/src" + export MOLTEMPLATE_PATH="$HOME/moltemplate/common" +If you use the tcsh shell, typically you would edit your +~/.login, ~/.cshrc, or ~/.tcshrc files to contain the following lines: + setenv PATH "$PATH:$HOME/moltemplate/src" + setenv MOLTEMPLATE_PATH "$HOME/moltemplate/common" + + -- Requirements: -- + +Moltemplate requires the Bourne-shell, and a recent version of python +(2.7, 3.0 or higher), and can run on OS X, linux, or windows (if a +suitable shell environment has been installed). + + -- License: -- + +Moltemplate is available under the terms of the open-source 3-clause BSD +license. (See LICENSE.TXT.) diff --git a/tools/moltemplate/common/graphene.lt b/tools/moltemplate/common/graphene.lt new file mode 100644 index 0000000000..4a17862fc3 --- /dev/null +++ b/tools/moltemplate/common/graphene.lt @@ -0,0 +1,106 @@ +# This file contains a unit cell for building graphene and nanotubes +# +# +# The 2AtomCellAlignX "molecule" defined below is a minimal unit cell for any +# hexagonal tesselation in 2-dimensions. (See "graphene_unit_cell.jpg") +# Surfaces constructed with this unit cell can be flat or curved into tubes. +# The distance between nearest-neighbor carbon atoms (ie the length of a +# carbon-carbon bond) is equal to "d" which I set to 1.420 Angstroms. +# +# d = length of each hexagon's side = 1.42 Angstroms +# L = length of each hexagon = 2*d = 2.84 Angstroms +# W = width of each hexagon = 2*d*sqrt(3)/2 = 2.4595121467478056 Angstroms +# +# Consequently, the Lattice-cell vectors for singe-layer graphene are: +# (2.4595121467478, 0, 0) (aligned with X axis) +# (1.2297560733739, 2.13, 0) (2.13 = 1.5*d) +# So, to build a sheet of graphite, you could use: +# sheet = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0) +# [10].move(1.2297560733739,2.13,0) + + + + +Graphene { + + 2AtomCellAlignX + { + # atomID molID atomType charge x y z + write("Data Atoms") { + $atom:C1 $mol:... @atom:../C 0.0 -0.61487803668695 -0.355 0.0 + $atom:C2 $mol:... @atom:../C 0.0 0.61487803668695 0.355 0.0 + } + } + + # Now define properties of the Carbon graphene atom + + write_once("In Init") { + pair_style hybrid lj/charmm/coul/charmm 9.0 10.0 + } + + write_once("Data Masses") { + @atom:C 12.0 + } + + write_once("In Settings") { + # i j epsilon sigma + pair_coeff @atom:C @atom:C lj/charmm/coul/charmm 0.068443 3.407 + + # These Lennard-Jones parameters come from + # R. Saito, R. Matsuo, T. Kimura, G. Dresselhaus, M.S. Dresselhaus, + # Chem Phys Lett, 348:187 (2001) + + # Define a group consisting of only carbon atoms in graphene molecules + group Cgraphene type @atom:C + } + + # Notice that the two atoms in the unit-cell above lie in the XY plane. + # (Their z-coordinate is zero). It's also useful to have a version of + # this object which lies in the XZ plan. So we define this below: + + 2AtomCellAlignXZ = 2AtomCellAlignX.rot(90,1,0,0) + +} # Graphene + + + + + + + + + + +# ------------ Graphite ----------- +# +# Note: For graphite: sheets stacked in the Z direction are separated by a +# distance of 3.35 Angstroms, and shifted in an alternating +/-Y direction +# by a distance of d (1.42 Angstroms). To add additional graphene layers +# you could use: +# sheet2 = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0) +# [10].move(1.2297560733739,2.13,0) +# sheet2[*][*].move(0, 1.42, 3.35) +# sheet3 = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0) +# [10].move(1.2297560733739,2.13,0) +# sheet3[*][*].move(0, -1.42, 6.70) +# etc... +# However, to build a thick sheet of graphite, it would +# be more efficient to use a 4-atom unit cell: +# +#Graphene { +# GraphiteCell { +# # atomID molID atomType charge x y z +# write("Data Atoms") { +# $atom:C1 $mol:... @atom:../C 0.0 -0.61487803668695 -0.355 0.0 +# $atom:C2 $mol:... @atom:../C 0.0 0.61487803668695 0.355 0.0 +# $atom:C3 $mol:... @atom:../C 0.0 -0.61487803668695 1.065 3.35 +# $atom:C4 $mol:... @atom:../C 0.0 0.61487803668695 1.775 3.35 +# } +# } # GraphiteCell +#} +# +# Then you could create a thick sheet of graphite this way: +# +# graphite = new Graphene/GraphiteCell [10].move(2.4595121467478,0,0) +# [10].move(1.2297560733739,2.13,0) +# [5].move(0,0,6.70) diff --git a/tools/moltemplate/common/images/graphene_unit_cell.jpg b/tools/moltemplate/common/images/graphene_unit_cell.jpg new file mode 100644 index 0000000000..12dbf8fca2 Binary files /dev/null and b/tools/moltemplate/common/images/graphene_unit_cell.jpg differ diff --git a/tools/moltemplate/common/images/ice_rect8_unitcell.png b/tools/moltemplate/common/images/ice_rect8_unitcell.png new file mode 100644 index 0000000000..5bd6057e1e Binary files /dev/null and b/tools/moltemplate/common/images/ice_rect8_unitcell.png differ diff --git a/tools/moltemplate/common/images/spce_ball_and_stick.jpg b/tools/moltemplate/common/images/spce_ball_and_stick.jpg new file mode 100644 index 0000000000..60aaf90b95 Binary files /dev/null and b/tools/moltemplate/common/images/spce_ball_and_stick.jpg differ diff --git a/tools/moltemplate/common/spce.lt b/tools/moltemplate/common/spce.lt new file mode 100644 index 0000000000..2b550b6309 --- /dev/null +++ b/tools/moltemplate/common/spce.lt @@ -0,0 +1,52 @@ +# file "spce.lt" +# +# H1 H2 +# \ / +# O + +SPCE { + + write_once("In Init") { + # -- Default styles (for solo "SPCE" water) -- + units real + atom_style full + # (Hybrid force fields were not necessary but are used for portability.) + pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 + bond_style hybrid harmonic + angle_style hybrid harmonic + kspace_style pppm 0.0001 + pair_modify mix arithmetic + } + + write("Data Atoms") { + $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 + $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 + $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590 + } + + write_once("Data Masses") { + @atom:O 15.9994 + @atom:H 1.008 + } + + write("Data Bonds") { + $bond:OH1 @bond:OH $atom:O $atom:H1 + $bond:OH2 @bond:OH $atom:O $atom:H2 + } + + write("Data Angles") { + $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 + } + + write_once("In Settings") { + bond_coeff @bond:OH harmonic 1000.0 1.0 + angle_coeff @angle:HOH harmonic 1000.0 109.47 + pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 + pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058 + group spce type @atom:O @atom:H + fix fSHAKE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH + # (Remember to "unfix" fSHAKE during minimization.) + } + +} # end of definition of "SPCE" water molecule type + diff --git a/tools/moltemplate/common/spce_ice_rect8.lt b/tools/moltemplate/common/spce_ice_rect8.lt new file mode 100644 index 0000000000..ccfd2f18c6 --- /dev/null +++ b/tools/moltemplate/common/spce_ice_rect8.lt @@ -0,0 +1,57 @@ +# This ice (1h) unit cell is rectangular and contains 8 water molecules. +# (Coordinates and cell dimensions converted were from a PDB file.) +# The dimensions of the unit cell (in Angstroms) are: 4.521 7.832 7.362 + + +import "spce.lt" # <-- define the "SPCE" molecule + +SpceIceRect8 { + + # Create a 3-dimensional array of 8 water molecules + + wat = new SPCE[2][2][2] + + # Array indices will be correlated with position [xindex][yindex][zindex] + + # You can overwrite coordinates of atoms after they were created this way: + # (Order is not important) + # atom-ID molecule-ID atomType charge newX newY newZ + + write("Data Atoms") { + $atom:wat[1][0][0]/O $mol:wat[1][0][0] @atom:SPCE/O -0.8476 3.391 1.305 1.381 + $atom:wat[1][0][0]/H1 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 3.391 0.370 1.710 + $atom:wat[1][0][0]/H2 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 2.582 1.772 1.710 + $atom:wat[1][0][1]/O $mol:wat[1][0][1] @atom:SPCE/O -0.8476 3.391 1.305 5.981 + $atom:wat[1][0][1]/H1 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 3.391 1.305 6.970 + $atom:wat[1][0][1]/H2 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 4.200 1.772 5.652 + $atom:wat[0][0][0]/O $mol:wat[0][0][0] @atom:SPCE/O -0.8476 1.131 2.611 2.300 + $atom:wat[0][0][0]/H1 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 1.131 2.611 3.289 + $atom:wat[0][0][0]/H2 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 0.320 2.143 1.971 + $atom:wat[0][0][1]/O $mol:wat[0][0][1] @atom:SPCE/O -0.8476 1.131 2.611 5.061 + $atom:wat[0][0][1]/H1 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.940 2.143 5.391 + $atom:wat[0][0][1]/H2 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.131 3.546 5.391 + $atom:wat[0][1][0]/O $mol:wat[0][1][0] @atom:SPCE/O -0.8476 1.131 5.221 1.381 + $atom:wat[0][1][0]/H1 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.131 4.286 1.710 + $atom:wat[0][1][0]/H2 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 0.320 5.688 1.710 + $atom:wat[0][1][1]/O $mol:wat[0][1][1] @atom:SPCE/O -0.8476 1.131 5.221 5.981 + $atom:wat[0][1][1]/H1 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.131 5.221 6.970 + $atom:wat[0][1][1]/H2 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.940 5.688 5.652 + $atom:wat[1][1][0]/O $mol:wat[1][1][0] @atom:SPCE/O -0.8476 3.391 6.526 2.300 + $atom:wat[1][1][0]/H1 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 3.391 6.526 3.289 + $atom:wat[1][1][0]/H2 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 2.582 6.058 1.971 + $atom:wat[1][1][1]/O $mol:wat[1][1][1] @atom:SPCE/O -0.8476 3.391 6.526 5.061 + $atom:wat[1][1][1]/H1 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 4.200 6.058 5.391 + $atom:wat[1][1][1]/H2 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 3.391 7.462 5.391 + } +} # IceRect8 + +# Credit goes to Martin Chaplin. +# These coordinates were orignally downloaded from Martin Chaplin's +# website: http://www.btinternet.com/~martin.chaplin/ice1h.html +# ... and then they were stretched independently in the xy and z +# directions in order to match the lattice parameters measured by +# Rottger et al., +# "Lattice constants and thermal expansion of H2O and D2O ice Ih" +# between 10 and 265K", Acta Crystallogr. B, 50 (1994) 644-648 +# I am using the lattice constants measured at temperature 265K +# (and pressure=100Torr). diff --git a/tools/moltemplate/common/tip3p_attempts/README.TXT b/tools/moltemplate/common/tip3p_attempts/README.TXT new file mode 100644 index 0000000000..13a2626d42 --- /dev/null +++ b/tools/moltemplate/common/tip3p_attempts/README.TXT @@ -0,0 +1,13 @@ +This directory contains two LT files corresponding to +different versions of TIP3P: + +tip3pcharmm.lt # The implementation of TIP3P used by CHARMM (I think). +tip3p2004.lt # The newer Price & Brooks, J. Chem Phys 2004 model + # which uses long-range coulombics + +I have not tested these files so I moved them here. +(If you have tested these files, and they work, or if you have other comments +or suggestions, feel free to email me at jewett.aij at gmail dot com.) + +Andrew +2012-10-20 diff --git a/tools/moltemplate/common/tip3p_attempts/tip3p2004.lt b/tools/moltemplate/common/tip3p_attempts/tip3p2004.lt new file mode 100644 index 0000000000..f04a161b35 --- /dev/null +++ b/tools/moltemplate/common/tip3p_attempts/tip3p2004.lt @@ -0,0 +1,88 @@ +# file "tip3p2004.lt" +# +# H1 H2 +# \ / +# O +# +# I think this is the TIP3P water described in the paper by +# Daniel J. Price and Charles L. Brooks III +# J. Chem. Phys., 121(20): 10096 (2004) +# Specifically I think it refers to the "Model B" version of long-range TIP3P +# described in the 3rd-to-last column of "Table I", on p.10099. + +TIP3P2004 { + + write_once("In Init") { + # -- Default styles (for solo "TIP3P2004" water) -- + units real + atom_style full + + pair_style hybrid lj/charmm/coul/long 10.0 10.5 10.5 + bond_style hybrid harmonic + angle_style hybrid harmonic + kspace_style pppm 0.0001 + pair_modify mix arithmetic + } + + write("Data Atoms") { + $atom:O $mol:. @atom:O -0.830 0.0000000 0.00000 0.000000 + $atom:H1 $mol:. @atom:H 0.415 0.756950327 0.00000 0.5858822766 + $atom:H2 $mol:. @atom:H 0.415 -0.756950327 0.00000 0.5858822766 + } + + write_once("Data Masses") { + @atom:O 15.9994 + @atom:H 1.008 + } + + write("Data Bonds") { + $bond:OH1 @bond:OH $atom:O $atom:H1 + $bond:OH2 @bond:OH $atom:O $atom:H2 + } + + write("Data Angles") { + $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 + } + + write_once("In Settings") { + bond_coeff @bond:OH harmonic 450.0 0.9572 + angle_coeff @angle:HOH harmonic 55.0 104.52 + + ######################################################################### + #### There are two choices for for the O-O interactions + ######################################################################### + #### O-O nonbonded interactions + # For the 1983 Jorgensen version of TIP3P use: + # pair_coeff @atom:O @atom:O lj/charmm/coul/charmm 0.1521 3.1507 + # For the 2004 Price & Brooks version of TIP3P use: + pair_coeff @atom:O @atom:O lj/charmm/coul/charmm 0.102 3.188 + ######################################################################### + #### There are three choices for for the O-H and H-H interactions + ######################################################################### + #### 1) CHARMM uses an arithmetic mixing-rule for the O-H sigma parameter + pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.0460 0.4000 + pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.7753 #arithmetic + ######################################################################### + #### 2) OPLS-AA uses geometric a mixing-fule for the O-H sigma parameter, + #### If you want to use this, uncomment the following two lines: + # pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.0460 0.4000 + # pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.1226 #geometric + ######################################################################### + #### 3) The original Jorgensen 1983 parameterization has no OH or HH + # lennard-jones interactions. For this behavior, uncomment these lines: + # pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.00 0.4000 + # pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.00 1.7753 + ######################################################################### + + # Define a group for the tip3p water molecules: + group tip3p type @atom:O @atom:H + + # Optional: Constrain the angles and distances. + # (Most implementations use this, but it is optional.) + fix fSHAKE tip3p shake 0.0001 10 100 b @bond:OH a @angle:HOH + # (Remember to "unfix" fSHAKE during minimization.) + + } + +} # "TIP3P2004" water molecule type + diff --git a/tools/moltemplate/common/tip3p_attempts/tip3pcharmm.lt b/tools/moltemplate/common/tip3p_attempts/tip3pcharmm.lt new file mode 100644 index 0000000000..80ea280fa5 --- /dev/null +++ b/tools/moltemplate/common/tip3p_attempts/tip3pcharmm.lt @@ -0,0 +1,91 @@ +# file "tip3p_charmm.lt" +# +# H1 H2 +# \ / +# O +# +# I think this is the TIP3P water model used by CHARMM (and probably AMBER) +# It is (mostly) based on this paper: +# Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem Phys, 79, 926 (1983) + +TIP3Pcharmm { + + write_once("In Init") { + # -- Default styles (for solo "TIP3Pcharmm" water) -- + units real + atom_style full + + # I'm not sure exactly which cutoffs distances are traditionally used in + # the TIP3P water model used by CHARMM. + # (See the Price JCP 2004 paper for a review.) + # pair_style hybrid lj/charmm/coul/charmm 7.5 8.0 10.0 10.5 + # Try this instead: + pair_style hybrid lj/charmm/coul/charmm 10.0 10.5 10.0 10.5 + + bond_style hybrid harmonic + angle_style hybrid harmonic + pair_modify mix arithmetic + } + + write("Data Atoms") { + $atom:O $mol:. @atom:O -0.834 0.0000000 0.00000 0.000000 + $atom:H1 $mol:. @atom:H 0.417 0.756950327 0.00000 0.5858822766 + $atom:H2 $mol:. @atom:H 0.417 -0.756950327 0.00000 0.5858822766 + } + + write_once("Data Masses") { + @atom:O 15.9994 + @atom:H 1.008 + } + + write("Data Bonds") { + $bond:OH1 @bond:OH $atom:O $atom:H1 + $bond:OH2 @bond:OH $atom:O $atom:H2 + } + + write("Data Angles") { + $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 + } + + write_once("In Settings") { + bond_coeff @bond:OH harmonic 450.0 0.9572 + angle_coeff @angle:HOH harmonic 55.0 104.52 + + ######################################################################### + #### There are two choices for for the O-O interactions + ######################################################################### + #### O-O nonbonded interactions + # For the 1983 Jorgensen version of TIP3P use: + pair_coeff @atom:O @atom:O lj/charmm/coul/charmm 0.1521 3.1507 + # For the 2004 Price & Brooks version of TIP3P use: + # pair_coeff @atom:O @atom:O lj/charmm/coul/charmm 0.102 3.188 + ######################################################################### + #### There are three choices for for the O-H and H-H interactions + ######################################################################### + #### 1) CHARMM uses an arithmetic mixing-rule for the O-H sigma parameter + pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.0460 0.4000 + pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.7753 #arithmetic + ######################################################################### + #### 2) OPLS-AA uses geometric a mixing-fule for the O-H sigma parameter, + #### If you want to use this, uncomment the following two lines: + # pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.0460 0.4000 + # pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.1226 #geometric + ######################################################################### + #### 3) The original Jorgensen 1983 parameterization has no OH or HH + # lennard-jones interactions. For this behavior, uncomment these lines: + # pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.00 0.4000 + # pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.00 1.7753 + ######################################################################### + + # Define a group for the tip3p water molecules: + group tip3p type @atom:O @atom:H + + # Optional: Constrain the angles and distances. + # (Most implementations use this, but it is optional.) + fix fSHAKE tip3p shake 0.0001 10 100 b @bond:OH a @angle:HOH + # (Remember to "unfix" fSHAKE during minimization.) + + } + +} # "TIP3Pcharmm" water molecule type + diff --git a/tools/moltemplate/common/trappe1998.lt b/tools/moltemplate/common/trappe1998.lt new file mode 100644 index 0000000000..9bcc80cb1c --- /dev/null +++ b/tools/moltemplate/common/trappe1998.lt @@ -0,0 +1,50 @@ +# This file stores complete LAMMPS data for the TraPPE model of saturated +# hydrocarbon chains. In this "united-atom" model, each methyl group is +# represented by a single atom. Forces between "atoms" are taken from the +# TraPPE force-field. (J Phys Chem B, 1998, volume 102, pp.2569-2577) + +TraPPE { + + write_once("In Init") { + # -- Default styles for "TraPPE" -- + units real + atom_style full + # (Hybrid force field styles were used for portability.) + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid opls + improper_style none + pair_style hybrid lj/charmm/coul/charmm 9.0 11.0 9.0 11.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom:CH2 14.1707 + @atom:CH3 15.2507 + @atom:CH4 16.3307 + } + + write_once("Data Angles By Type") { + @angle:backbone @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated + } + + write_once("Data Dihedrals By Type") { + @dihedral:backbone @atom:CH? @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated @bond:saturated + } + + write_once("In Settings") { + pair_coeff @atom:CH2 @atom:CH2 lj/charmm/coul/charmm 0.091411522 3.95 + pair_coeff @atom:CH3 @atom:CH3 lj/charmm/coul/charmm 0.194746286 3.75 + pair_coeff @atom:CH4 @atom:CH4 lj/charmm/coul/charmm 0.294106636 3.73 + bond_coeff @bond:saturated harmonic 120.0 1.54 + angle_coeff @angle:backbone harmonic 62.0022 114 + dihedral_coeff @dihedral:backbone opls 1.411036 -0.271016 3.145034 0.0 + } + + write_once("In Settings") { + group TraPPE type @atom:CH2 @atom:CH3 @atom:CH4 + } + +} # class TraPPE + diff --git a/tools/moltemplate/common/watmw.lt b/tools/moltemplate/common/watmw.lt new file mode 100644 index 0000000000..c7aaecebbc --- /dev/null +++ b/tools/moltemplate/common/watmw.lt @@ -0,0 +1,54 @@ +# This file stores LAMMPS data for the "mW" water model. +# (Molinero, V. and Moore, E.B., J. Phys. Chem. B 2009, 113, 4008-4016) +# +# In this model, each water molecule is represented by a single "mW" particle. +# These particles interact with their neighbors via 3-body Stillinger-Weber +# forces whose parameters are tuned to mimic directional hydrogen-bonding +# in liquid water (as well as hexagonal ice, type II ice, and +# low-density super-cooled liquid/amorphous water phases). + +WatMW { + write("Data Atoms") { + $atom:mW $mol:. @atom:mW 0.0 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom:mW 18.02 + } + + write_once("system.in.sw") { + mW mW mW 6.189 2.3925 1.8 23.15 1.2 -0.333333333 7.049556277 0.602224558 4 0 0 + } + + write_once("In Init") { + # -- Default styles for "WatMW" -- + units real + pair_style sw + } + + write_once("In Settings") { + # --Now indicate which atom type(s) are simulated using the "sw" pair style + # -- In this case only one of the atom types is used (the mW water "atom"). + + pair_coeff * * sw system.in.sw mW NULL NULL NULL + + # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so + # -- the atoms are identified by order in the list, not by name. (The "mW" + # -- refers to to an identifier in the system.in.sw file, not watmw.lt.) + # -- This command says that the first atom type corresponds to the "mW" + # -- atom in system.in.sw, and to ignore the remaining three atom types + # -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt. + # -- We don't want to use the "sw" force field for interactions involving + # -- these atom types, so we put "NULL" there.) + # -- Note: For this to work, you should probably run moltemplate this way: + # -- moltemplate.sh -a "@atom:WatMW/mW 1" system.lt + # -- This assigns the atom type named @atom:WatMW/mW to 1 (the first atom) + } + + # -- optional -- + + write_once("In Settings") { + group WatMW type @atom:mW #(Atoms of this type belong to the "WatMW" group) + } + +} # WatMW diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README.TXT b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README.TXT new file mode 100644 index 0000000000..09abbc4b2a --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README.TXT @@ -0,0 +1,70 @@ + This example shows how to put a protein (inclusion) in a + lipid bilayer mixture composed of two different lipids (DPPC and DLPC). + The DPPC lipid model is described here: + G. Brannigan, P.F. Philips, and F.L.H. Brown, + Physical Review E, Vol 72, 011915 (2005) + (The DLPC model is a truncated version of DPPC. Modifications discussed below.) + The protein model is described here: + G. Bellesia, AI Jewett, and J-E Shea, + Protein Science, Vol19 141-154 (2010) + +--- PREREQUISITES: --- + +1) This example requires the "dihedral_style fourier", which is currently +in the USER-MISC package. Build LAMMPS with this package enabled using + make yes-user-misc +before compiling LAMMPS. +(See http://lammps.sandia.gov/doc/Section_start.html#start_3 for details.) + +2) This example may require additional features to be added to LAMMPS. +If LAMMPS complains about an "Invalid pair_style", then + a) download the "additional_lammps_code" from + http://moltemplate.org (upper-left corner menu) + b) unpack it + c) copy the .cpp and .h files to the src folding of your lammps installation. + d) (re)compile LAMMPS. + + +----- Details -------- + +This example contains a coarse-grained model of a 4-helix bundle protein +inserted into a lipid bilayer (made from a mixture of DPPC and DLPC). + + -- Protein Model: -- + +The coarse-grained protein is described in: + G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) +Here we use the "AUF2" model described in that paper. +(The hydrophobic beads face outwards.) + + -- Memebrane Model: -- + +The DPPC lipid bilayer described in: + G. Brannigan, P.F. Philips, and F.L.H. Brown, + Physical Review E, Vol 72, 011915 (2005) +and: + M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown + J. Chem. Phys. 135, 244701 (2011) + +As in Watson(JCP 2011), rigid bond-length constraints +have been replaced by harmonic bonds. + +A truncated version of this lipid (named "DLPC") has also been added. +The bending stiffness of each lipid has been increased to compensate +for the additional disorder resulting from mixing two different types +of lipids together. (Otherwise pores appear.) +Unlike the original "DPPC" molecule model, the new "DPPC" and "DLPC" models +have not been carefully parameterized to reproduce the correct behavior in +a lipid bilayer mixture. + + +------------- + +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_run.sh new file mode 100755 index 0000000000..9598e3b08d --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_run.sh @@ -0,0 +1,33 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The "run.in.nvt" file is a LAMMPS input script containing +# references to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data, and table_int.dat +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.npt # Run a simulation at constant pressure (tension) + +#or + +lmp_linux -i run.in.nvt # Run a simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation are ignored when beginning the simulation at constant volume. +# This can be fixed. Read "run.in.nvt" for equilibration instructions.) + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.npt +#or +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_setup.sh new file mode 100755 index 0000000000..abf2fce64b --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_setup.sh @@ -0,0 +1,28 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # The "table_int.dat" file contains tabular data for the lipid INT-INT atom + # 1/r^2 interaction. We need it too. (This slows down the simulation by x2, + # so I might look for a way to get rid of it later.) + cp -f table_int.dat ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg new file mode 100644 index 0000000000..246ee54625 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 0000000000..cf5ef4faf5 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,2611 @@ +PSF + + 1 !NTITLE + REMARKS VMD-generated NAMD/X-Plor PSF structure file + + 1685 !NATOM + 1 1 "head" 4 4 0.000000 200.0000 0 + 2 1 2 2 0.000000 200.0000 0 + 3 1 3 3 0.000000 200.0000 0 + 4 1 3 3 0.000000 200.0000 0 + 5 2 "head" 1 1 0.000000 200.0000 0 + 6 2 2 2 0.000000 200.0000 0 + 7 2 3 3 0.000000 200.0000 0 + 8 2 3 3 0.000000 200.0000 0 + 9 2 3 3 0.000000 200.0000 0 + 10 3 "head" 1 1 0.000000 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differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_no_pbc_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_no_pbc_LR.jpg new file mode 100644 index 0000000000..142f3f706f Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_no_pbc_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_top_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_top_LR.jpg new file mode 100644 index 0000000000..5d4b15b291 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_top_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=5000ps_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=5000ps_LR.jpg new file mode 100644 index 0000000000..285389039d Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=5000ps_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010.lt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010.lt new file mode 100644 index 0000000000..a5df81056d --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010.lt @@ -0,0 +1,254 @@ +# This file defines a 4-helix bundle coarse-grained protein model (AUF2) used in +# G. Bellesia, AI Jewett, and J-E Shea, +# Protein Science, Vol19 141-154 (2010) +# +# Strategy: +# +#1) First I'll define some building blocks (A16, B16, T3) +# which are helices, sheets and turns of a predetermined length) +# +#2) Then I'll copy and paste them together to build +# a 4-helix bundle (or a 4-strand beta-barrel). +# This approach is optional. If your protein has helices which are not +# identical, you should probably just include all 4 helices in a single +# "Data Atoms" section and don't try to subdivide the protein into pieces.) + + + +1beadProtSci2010 { # <-- enclose definitions in a namespace for portability + + # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each) + + A16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../sL 0.0 -2.4 -2.4 0.0 + $atom:a2 $mol:... @atom:../sL 0.0 2.4 -2.4 3.6 + $atom:a3 $mol:... @atom:../sH 0.0 2.4 2.4 7.2 + $atom:a4 $mol:... @atom:../sH 0.0 -2.4 2.4 10.8 + $atom:a5 $mol:... @atom:../sL 0.0 -2.4 -2.4 14.4 + $atom:a6 $mol:... @atom:../sL 0.0 2.4 -2.4 18.0 + $atom:a7 $mol:... @atom:../sH 0.0 2.4 2.4 21.6 + $atom:a8 $mol:... @atom:../sH 0.0 -2.4 2.4 25.2 + $atom:a9 $mol:... @atom:../sL 0.0 -2.4 -2.4 28.8 + $atom:a10 $mol:... @atom:../sL 0.0 2.4 -2.4 32.4 + $atom:a11 $mol:... @atom:../sH 0.0 2.4 2.4 36.0 + $atom:a12 $mol:... @atom:../sH 0.0 -2.4 2.4 39.6 + $atom:a13 $mol:... @atom:../sL 0.0 -2.4 -2.4 43.2 + $atom:a14 $mol:... @atom:../sL 0.0 2.4 -2.4 46.8 + $atom:a15 $mol:... @atom:../sH 0.0 2.4 2.4 50.4 + $atom:a16 $mol:... @atom:../sH 0.0 -2.4 2.4 54.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # A16 + + + T3 { # T3 is a "turn" region consisting of 3 beads + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../tN 0.0 -4.8 0.0 0.0 + $atom:a2 $mol:... @atom:../tN 0.0 0.0 3.3 -1.44 + $atom:a3 $mol:... @atom:../tN 0.0 4.8 0.0 0.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + } + + } # T3 + + + # ----- Now build a larger molecule using A16 and T3 ------- + + # Create a 4-Helix bundle. + # In this version, the hydrophobic beads are poing outward. + # I oriented them this way because I want to place this protein in a membrane. + # (There is another file in this directory containing alternate version + # of this same molecule with the hydrophobic beads pointing inward.) + + 4HelixInsideOut { + helix1 = new A16.rot(-225, 0,0,1).move(-5.70,-5.70,-32.4) + helix2 = new A16.rot(-135, 0,0,1).move( 5.70,-5.70,-28.8) + helix3 = new A16.rot( -45, 0,0,1).move( 5.70, 5.70,-25.2) + helix4 = new A16.rot( 45, 0,0,1).move(-5.70, 5.70,-21.6) + + turn1 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot( 10,0,0,1).move(0.78,-4.2, 27.9) + turn2 = new T3.rot(-10,1,0,0).rot( 20,0,1,0).rot(-70,0,0,1).move(4.55, 2.4,-33.0) + turn3 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot(190,0,0,1).move(-0.78,4.2, 34.2) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + + } # 4HelixInsideOut + + + # -------- Minor coordinates adjustment: ----------- + + # Those coordinates in the commands above are a little too large. + # To make it easier to type them in, I was using sigma=6.0 Angstroms. + # Instead, here I'll try using sigma=5.5 Angstroms. 5.5/6 = 0.916667) + + 4HelixInsideOut.scale(0.9166666666666666) + + # Note: "scale()" only effects the initial coordinates of + # the molecule, not the force field parameters. + # (If you plan to minimize the molecule, you don't need to + # be so careful about the initial coordinates. In that case, + # you don't have worry about "scale()". Feel free to remove.) + + + + # -------------- Force-Field Parameters ------------ + + # Units and force-field styles for this protein model + # (These can be overridden later.) + + write_once("In Init") { + units real + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid fourier + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 21.0 24.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + + # --- Distance Units --- + # In this version of the model, sigma (the bond-length + # and particle diameter) is rounded to 5.5 Angstroms. + # + # --- Energy & Temperature Units --- + # In this protein model, "epsilon" represents the free energy + # bonus for bringing two hydrophobic amino acids together. + # Here I choose to set epsilon to 1.806551818181818 kCal/mole. + # This value was chosen so that a temperature of 300 Kelvin lies at + # 0.33 epsilon, which is the unfolding temperature of the marginally stable + # "ASF1" protein model from the Bellesia et al 2010 paper. + # This choice insures that both the "ASF1" model from that paper, + # as well as the much more stable "AUF2" protein we use here (which + # unfolds at 0.42*eps) should definitely remain stable at 300 degrees Kelvin, + # in the bulk at least. (However it's not clear that these energy + # parameters will work well for a protein in membrane. Perhaps I'll + # run some tests and fine tune these parameters for this scenario.) + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:sH @atom:sH lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 + pair_coeff @atom:sL @atom:sL lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0 + pair_coeff @atom:tN @atom:tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0 + } + + # The exact value of the bond_coeff does not matter too much as long as + # it is "stiff enough". Here I use a softer bond spring than the one + # used in the paper so that I can increase the time step. + # I also use a relatively soft spring to constrain the bond angles. + + # bond_coeff bondType bondstylename k r0 + + write_once("In Settings") { + bond_coeff @bond:1beadProtSci2010/backbone harmonic 10.0 5.5 + } + + + + # We use the same bond-angle forces whenever + # there are 3 consecutively-bonded atoms: + # + # angleType atomtypes1 2 3 bondtypes1 2 + + write_once("Data Angles By Type") { + @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* + } + + # angle_coeff angleType anglestylename k theta0 + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 100.0 105.0 + } + + + + + # Dihedral interactions are also determined by atom-type name in this case. + # I chose atoms whose type-names begin with "t" to be "turn" atoms. + # Atoms whose type-names begin with "s" could be either helices or sheets. + # (In this case, helices. In this example, we use the @dihedral:delta65_0 + # parameters. This corresponds to the "AUF2" model from the + # Bellesia et. al 2010 paper.) + + # dihedralType atomtypes1 2 3 4 bondtypes1 2 3 + + write_once("Data Dihedrals By Type") { + @dihedral:delta65_0 @atom:s* @atom:s* @atom:s* @atom:s* * * * + + # If "tN" (turn) atoms are present, use the @dihedral:turn parameters + + @dihedral:turn @atom:tN @atom:* @atom:* @atom:* * * * + } + + + # From the Bellesia et al 2010 paper: + # for helices: U_{dih}(\phi) = 1.2*(cos(3\phi) + cos(\phi+\delta)) + # for turns: U_{dih}(\phi) = 0.2*cos(3\phi) + # + # General formula used for "dihedral_style fourier": + # U_{dih}(\phi) = \Sum_{i=1}^m K_i [ 1.0 + cos(n_i \phi - d_i) ] + # + # Syntax: + # dihedralType dihedralstyle m K_1 n_1 d_1 K2 n_2 d_2 ... + + write_once("In Settings") { + dihedral_coeff @dihedral:delta60_0 fourier 2 2.167862 3 0 2.167862 1 -60.0 + dihedral_coeff @dihedral:delta62_5 fourier 2 2.167862 3 0 2.167862 1 -62.5 + dihedral_coeff @dihedral:delta65_0 fourier 2 2.167862 3 0 2.167862 1 -65.0 + dihedral_coeff @dihedral:turn fourier 1 0.361310 3 0 + # Note: 2.167862=1.2*epsilon and 0.361310=0.2*epsilon. + } + + + # --- Mass Units --- + # Typical amino acids weigh approximately 110.0 grams/mole. (Rounding down): + write_once("Data Masses") { + @atom:1beadProtSci2010/sH 100.0 + @atom:1beadProtSci2010/sL 100.0 + @atom:1beadProtSci2010/tN 100.0 + } + +} # 1beadProtSci2010 (namespace) + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt new file mode 100644 index 0000000000..e6e6bced70 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt @@ -0,0 +1,225 @@ +### THIS FILE IS OPTIONAL AND IS NOT NECESSARY. IN THIS FILE, I DEFINED SOME ## +### ADDITIONAL PROTEIN TYPES FROM THE PAPER THAT I DID NOT USE IN THIS EXAMPLE## +# +# This file defines a family of coarse-grained protein models used in: +# G. Bellesia, AI Jewett, and J-E Shea, +# Protein Science, Vol19 141-154 (2010) +# +# Strategy: +# +#1) First I'll define some building blocks (A16, B16, T3) +# which are helices, sheets and turns of a predetermined length) + +import "1beadProtSci2010.lt" + +# We defined A16 and T3 earlier in "1beadPRotSci2010.lt" Will define B16 below +# +#2) Then I'll copy and paste them together to build +# a 4-helix bundle or a 4-strand beta-barrel. + + +1beadProtSci2010 { #<-- Add new molecules to existing namespace defined earlier + # This way we don't have to start from scratch. We can + # use all the atom types and angle settings defined earlier + + # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each) + + B16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../sL 0.0 -1.8 0.0 0.0 + $atom:a2 $mol:... @atom:../sH 0.0 1.8 0.0 4.8 + $atom:a3 $mol:... @atom:../sL 0.0 -1.8 0.0 9.6 + $atom:a4 $mol:... @atom:../sH 0.0 1.8 0.0 14.4 + $atom:a5 $mol:... @atom:../sL 0.0 -1.8 0.0 19.2 + $atom:a6 $mol:... @atom:../sH 0.0 1.8 0.0 24.0 + $atom:a7 $mol:... @atom:../sL 0.0 -1.8 0.0 28.8 + $atom:a8 $mol:... @atom:../sH 0.0 1.8 0.0 33.6 + $atom:a9 $mol:... @atom:../sL 0.0 -1.8 0.0 38.4 + $atom:a10 $mol:... @atom:../sH 0.0 1.8 0.0 43.2 + $atom:a11 $mol:... @atom:../sL 0.0 -1.8 0.0 48.0 + $atom:a12 $mol:... @atom:../sH 0.0 1.8 0.0 52.8 + $atom:a13 $mol:... @atom:../sL 0.0 -1.8 0.0 57.6 + $atom:a14 $mol:... @atom:../sH 0.0 1.8 0.0 62.4 + $atom:a15 $mol:... @atom:../sL 0.0 -1.8 0.0 67.2 + $atom:a16 $mol:... @atom:../sH 0.0 1.8 0.0 72.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # B16 + + # ----- Now build larger molecules using B16 and T3 ------- + + + 4SheetBarrel { + sheet1 = new B16.rot( 45, 0,0,1).move(-4.762203156,-4.762203156, -36.0) + sheet2 = new B16.rot( 135, 0,0,1).move( 4.762203156,-4.762203156, -36.0) + sheet3 = new B16.rot( 225, 0,0,1).move( 4.762203156, 4.762203156, -36.0) + sheet4 = new B16.rot( 315, 0,0,1).move(-4.762203156, 4.762203156, -36.0) + + turn1 = new T3.rot(180,1,0,0).rot( 0, 0,0,1).move( 0, -7.8, 39.6) + turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(4.2, 0.0,-41.4) + turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move( 0, 7.8, 39.6) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + } + + + # Below I define several alternate conformations of the"4HelixBundleInsideOut" + # molecule I defined earlier in "1beadProtSci2010.lt". Same molecule however. + + 4HelixBundle { + helix1 = new A16.rot( -45, 0,0,1).move(-5.70,-5.70,-32.4) + helix2 = new A16.rot( 45, 0,0,1).move( 5.70,-5.70,-28.8) + helix3 = new A16.rot( 135, 0,0,1).move( 5.70, 5.70,-25.2) + helix4 = new A16.rot( 225, 0,0,1).move(-5.70, 5.70,-21.6) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + + turn1 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot( 8,0,0,1).move(-3.6,-4.8,28.2) + turn2 = new T3.rot(-5,1,0,0).rot( 21,0,1,0).rot(-100,0,0,1).move(4.2,-0.66,-30.9) + turn3 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot(188,0,0,1).move(3.6,4.8,35.4) + + create_var { $mol } # molecule ID number shared by all atoms in this protein + + } # 4HelixBundle + + + + + # --- alternate conformations (same molecule) ---- + + # In the following version, the helices are oriented in a similar way, + # but they are separated a little further away from eachother. + + 4HelixBundleLoose { + + helix1 = new A16.rot( -45, 0,0,1).move(-6.7347723,-6.7347723, -27.0) + helix2 = new A16.rot( 45, 0,0,1).move( 6.7347723,-6.7347723, -27.0) + helix3 = new A16.rot( 135, 0,0,1).move( 6.7347723, 6.7347723, -27.0) + helix4 = new A16.rot( 225, 0,0,1).move(-6.7347723, 6.7347723, -27.0) + + turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-1.2,-4.2,32.4) + turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(4.2,-0.9,-28.8) + turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(1.2,4.2,32.4) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + } + + + # In following version, the helices are oriented in a similar way, + # but they are separated a little further away from eachother. + + 4HelixInsideOutLoose { + helix1 = new A16.rot(-225, 0,0,1).move(-6.7347723,-6.7347723, -27.0) + helix2 = new A16.rot(-135, 0,0,1).move( 6.7347723,-6.7347723, -27.0) + helix3 = new A16.rot( -45, 0,0,1).move( 6.7347723, 6.7347723, -27.0) + helix4 = new A16.rot( 45, 0,0,1).move(-6.7347723, 6.7347723, -27.0) + + turn1 = new T3.rot(180,1,0,0).rot( 10,0,0,1).move( 0.78,-4.2,28.8) + turn2 = new T3.rot( 70,1,0,0).rot(-70,0,0,1).move( 10.8,2.4,-28.2) + turn3 = new T3.rot(180,1,0,0).rot(190,0,0,1).move(-0.78,4.2,28.8) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + + } # 4HelixInsideOutLoose + + + + + # In the following version, the 4 helices are arranged next to each other, + # side-by-side, in a planar conformation (instead of a compact bundle). + + 4HelixPlanar { + helix1 = new A16.rot(-00, 0,0,1).move(0, 0, -27.0) + helix2 = new A16.rot( 00, 0,0,1).move(14.4, 0, -27.0) + helix3 = new A16.rot(-00, 0,0,1).move(28.8, 0, -27.0) + helix4 = new A16.rot( 00, 0,0,1).move(43.2, 0, -27.0) + + turn1 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move( 4.8, 0, 31.8) + turn2 = new T3.rot( 0,1,0,0).rot(180,0,0,1).move(19.2, 0,-31.8) + turn3 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move(34.6, 0, 31.8) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + + } # 4HelixPlanar + + + # -------- Minor coordinates adjustment: ----------- + # Those coordinates in the commands above are a little too large. + # To make it easier to type them in, I was using sigma=6.0 Angstroms. + # Instead, here I'll try using sigma=5.5 Angstroms. 5.5/6 = 0.916667) + + 4SheetBarrel.scale(0.9166666666666666) + 4HelixBundle.scale(0.9166666666666666) + 4HelixBundleLoose.scale(0.9166666666666666) + 4HelixInsideOutLoose.scale(0.9166666666666666) + 4HelixPlanar.scale(0.9166666666666666) + + # Note: "scale()" only effects the initial coordinates of + # the molecule, not the force field parameters. + # (If you plan to minimize the molecule, you don't need to + # be so careful about the initial coordinates. In that case, + # you don't have worry about "scale()". Feel free to remove.) + + +} # 1beadProtSci2010 (namespace) + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/CGLipidBr2005.lt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/CGLipidBr2005.lt new file mode 100644 index 0000000000..3b39048f7e --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/CGLipidBr2005.lt @@ -0,0 +1,198 @@ +# Note: +# +# This example may require additional features to be added to LAMMPS. If +# LAMMPS complains about an "Invalid pair_style", then download copy the +# "additional_lammps_code" from moltemplate.org, unpack it into your LAMMPS +# "src" directory and recompile LAMMPS. +# +# -------- Description -------- +# +# This example contains an implementation of the DPPC lipid bilayer described in +# G. Brannigan, P.F. Philips, and F.L.H. Brown, +# Physical Review E, Vol 72, 011915 (2005) +# and: +# M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown +# J. Chem. Phys. 135, 244701 (2011) +# +# As in Watson(JCP 2011), rigid bond-length constraints have been replaced +# by harmonic bonds. +# +# A truncated version of this lipid (named "DLPC") has also been added. +# Unlike the original "DPPC" molecule model, "DLPC" has not been carefully +# parameterized to reproduce the correct behavior in a lipid bilayer mixture. +# +# Units: +# +# The "epsilon" parameter in their model is approximately 2.75 kJ/mole +# ( = 0.657265774378585 kCal/mole, using 1kCal=4.184kJ) +# The "sigma" parameter corresponds to 7.5 angstroms. + + +CGLipidBr2005 { + + + write_once("In Init") { + # -- Default styles for "CGLipidBr2005" -- + units real + atom_style full + # (Hybrid force field styles were used for portability.) + bond_style hybrid harmonic + + #angle_style hybrid cosine/delta # <- used in the original article + angle_style hybrid harmonic # <- prevents unphysical acute angle turns + # Explanation: + # angle_style cosine/delta: U(theta) = k*(1-cos(theta-theta0)) + # angle_style harmonic: U(theta) = k*(theta-theta0)^2 + + dihedral_style none + improper_style none + pair_style hybrid table linear 1130 & + lj/charmm/coul/charmm/inter es4k4l 14.5 15 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" + + neighbor 2.0 multi # <- perhaps unnecessary + communicate multi # <- perhaps unnecessary + } + + + DPPC { + write("Data Atoms") { + $atom:h $mol:. @atom:head 0.0 0.00 0.00 33.75 # DPPC head atom + $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 26.25 + $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 18.75 + $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 11.25 + $atom:t3 $mol:. @atom:../tail 0.0 1.00 0.00 3.75 + } + write("Data Bonds") { + $bond:b1 @bond:../backbone $atom:h $atom:i + $bond:b2 @bond:../backbone $atom:i $atom:t1 + $bond:b3 @bond:../backbone $atom:t1 $atom:t2 + $bond:b4 @bond:../backbone $atom:t2 $atom:t3 + } + write("Data Angles") { + $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 + $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 + $angle:a3 @angle:../backbone $atom:t1 $atom:t2 $atom:t3 + } + + # Define properties of the local (lipid-specific) atom:head type atom: + write_once("Data Masses") { + @atom:head 200.0 + } + write_once("In Settings") { + pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + } + + } #DPPC + + + DLPC { + write("Data Atoms") { + $atom:h $mol:. @atom:head 0.0 0.00 0.00 30.00 # DLPC head atom + $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 22.50 + $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 15.00 + $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 7.50 + } + write("Data Bonds") { + $bond:b1 @bond:../backbone $atom:h $atom:i + $bond:b2 @bond:../backbone $atom:i $atom:t1 + $bond:b3 @bond:../backbone $atom:t1 $atom:t2 + } + write("Data Angles") { + $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 + $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 + } + # Define properties of the local (lipid-specific) atom:head type atom: + write_once("Data Masses") { + @atom:head 200.0 + } + write_once("In Settings") { + pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + } + } #DLPC + + + # Particles and properties shared by all lipid types: + + write_once("Data Masses") { + @atom:int 200.0 + @atom:tail 200.0 + @atom:head 200.0 #<- Default head type. We may override it later. + } + + write_once("In Settings") { + # -- Default settings/parameters for "CGLipidBr2005" -- + # (Hybrid bond & angle styles were used for portability.) + + # As in Watson(JCP 2011), rigid bond-length constraints + # have been replaced by harmonic bonds. + # The k_theta parameter should lie in between 5*epsilon and 10*epsilon. + bond_coeff @bond:backbone harmonic 116.847 7.5 #<--2*5000*eps/sig^2 + } + + write_once("In Settings") { + # cosine/delta: U(theta) = k*(1-cos(theta-theta0)) + #angle_coeff @angle:backbone cosine/delta 4.60086042 180 #<-- 7*eps + # harmonic: U(theta) = k*(theta-theta0)^2 not (k/2)*(theta-theta0)^2 + angle_coeff @angle:backbone harmonic 9.85898661 180 #<-->30*eps + } + # I use a stiffer bond-angle than the original Brannigan & Brown 2005 paper + # to attempt to compensate for the fact that here we are using a lipid + # mixture of DPPC and DLPC. (The mixture of lipids introduces a great deal + # of disorder into the bilayer which would not be present in a DPPC bilayer. + # This causes pores to form. Increasing the angle stiffness prevents this.) + + write_once("In Settings") { + + # The interaction of "atom:int" with other "atom:int" atoms is given by + # epsilon*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2), shifted and cutoff at + # r=3*sigma. This was implemented using pair_style table. + # Unfortunately, mixing lj/charmm and "table" pair styles in the same + # simulation is very inneficient. + + pair_coeff @atom:int @atom:int table table_int.dat INT + + # The interaction of tail beads with eachother is given by the formula below + # and with other atoms ...using Lorenz-Berthelot and "repulsive wins" rules: + # epsilon*(0.4*(sigma/r)^12 - 1.0*(sigma/r)^6), + pair_coeff @atom:tail @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 + pair_coeff @atom:int @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 + + # The interaction of head beads which all other beads is given by: + # epsilon*(0.4*(sigma/r)^12 - 0.0*(sigma/r)^6), + + pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + + } # write_once("In Settings") + + # Note: I divided epsilon by 4 to get "0.1643" because we are using the + # "es4k4l" coeffstyle, corresponding to U(r)=eps(4*K*(s/r)^12 + 4*L*(s/r)^6) + # (The "es4k4l" coeffstyle is the default.) Using this convention makes it + # easier to mix this coarse-grained lipid model with other molecular models. + + + +} # CGLipidBr2005 + + + + + + + + +# Note: This example has not been optimized for speed. +# +# Unfortunately, using both lj/charmm and "table" pair styles in the same +# simulation seems to be very inneficient. (The simulation is twice as slow +# as using only the "lj/charmm" pair styles for every pairwise interaction, +# ...and about 25% slower than using "table" for every pairwise interaction. +# However the lennard-jones pair styles support mixing, so we use them to +# make it easier to run these molecules with other molecules which don't use +# pair_table. I felt that portability was worth the extra 25% slow down.) + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py new file mode 100755 index 0000000000..1eb97e6454 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py @@ -0,0 +1,34 @@ +#!/usr/bin/env python + +# Calculate a table of pairwise energies and forces between "INT" atoms +# in the lipid membrane model described in +# Brannigan et al, Phys Rev E, 72, 011915 (2005) +# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) +# However it is truncated at rc2 = 22.5 (shifted upwards to maintain continuity) + +# The previous version included the repulsive core term +def U(r, eps, sigma): + return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) +def F(r, eps, sigma): + return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) +# We don't want to do that. Instead compute the core repulsion using a +# different pair_style and add the attractive term on top of it using the table. +# This way it the core repulsion acts as a default interaction with other atom +# types (using the new repulsive mixing rules). + +epsilon = 2.75/4.184 # kCal/mole +sigma = 7.5 +Rmin = 0.02 +Rmax = 22.6 +rcut = 22.5 +N = 1130 + +for i in range(0,N): + r = Rmin + i*(Rmax-Rmin)/(N-1) + U_r = U(r, epsilon, sigma) - U(rcut, epsilon, sigma) + F_r = F(r, epsilon, sigma) + if r > rcut: + U_r = 0.0 + F_r = 0.0 + print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py new file mode 100755 index 0000000000..32147e444a --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py @@ -0,0 +1,70 @@ +#!/usr/bin/env python + +# Calculate a table of pairwise energies and forces between "INT" atoms +# in the lipid membrane model described in +# Brannigan et al, Phys Rev E, 72, 011915 (2005) +# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) +# I realized later this is not what we want because although energy is conserved +# all enrgies are shifted with respect to energies used in the Brannigan paper +# (by 0.27 kCal/mole) and the later Watson JCP 2011 paper (by 0.224 kCal/mole). +# (So don't use this.) + +# Calculate and print a + +def S(r, rc1, rc2, derivative=False): + """ + Calculate the switching function S(r) which decays continuously + between 1 and 0 in the range from rc1 to rc2 (rc2>rc1): + S(r) = (rc2^2 - r^2)^2 * (rc2^2 + 2*r^2 - 3*rc1^2) / (rc2^2-rc1^2)^3 + I'm using the same smoothing/switching cutoff function used by the CHARMM + force-fields. (I'm even using the same code to implement it, taken + from lammps charmm/coul/charmm pair style, rewritten in python.) + + """ + assert(rc2>rc1) + rsq = r*r + rc1sq = rc1*rc1 + rc2sq = rc2*rc2 + denom_lj_inv = (1.0 / ((rc2sq-rc1sq)* + (rc2sq-rc1sq)* + (rc2sq-rc1sq))) + if rsq > rc2sq: + return 0.0 + elif rsq < rc1sq: + if derivative: + return 0.0 + else: + return 1.0 + else: + rc2sq_minus_rsq = (rc2sq - rsq) + rc2sq_minus_rsq_sq = rc2sq_minus_rsq * rc2sq_minus_rsq + if derivative: + return (12.0 * rsq * rc2sq_minus_rsq * (rsq-rc1sq) * denom_lj_inv) + else: + return (rc2sq_minus_rsq_sq * + (rc2sq + 2.0*rsq - 3.0*rc1sq) * denom_lj_inv) + + +def U(r, eps, sigma): + return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) + +def F(r, eps, sigma): + return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) + +epsilon = 2.75/4.184 # kCal/mole +sigma = 7.5 +Rmin = 0.02 +Rmax = 22.6 +Rc1 = 22.0 +Rc2 = 22.5 +N = 1130 + +for i in range(0,N): + r = Rmin + i*(Rmax-Rmin)/(N-1) + U_r = U(r, epsilon, sigma) + F_r = F(r, epsilon, sigma) + # Multiply U(r) & F(r) by the smoothing/switch function + U_r = U_r * S(r, Rc1, Rc2) + F_r = U_r * S(r, Rc1, Rc2, True) + F_r * S(r, Rc1, Rc2, False) + print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/system.lt new file mode 100644 index 0000000000..51a67b6d9f --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/system.lt @@ -0,0 +1,207 @@ +# Description: + +# This example shows how to put a protein (inclusion) in a +# lipid bilayer mixture composed of two different lipids (DPPC and DLPC). +# The DPPC lipid model is described here: +# G. Brannigan, P.F. Philips, and F.L.H. Brown, +# Physical Review E, Vol 72, 011915 (2005) +# The protein model is described here: +# G. Bellesia, AI Jewett, and J-E Shea, +# Protein Science, Vol19 141-154 (2010) +# The new DLPC model is a truncated version of DPPC, +# (Its behaviour has not been rigorously tested.) +# Note that 50%/50% mixtures of DPPC & DLPC are commonly used to +# build liposomes http://www.ncbi.nlm.nih.gov/pubmed/10620293 + +# Note: +# This example may require additional features to be added to LAMMPS. +# If LAMMPS complains about an "Invalid pair_style", then copy the code +# in the "additional_lammps_code" directory into your LAMMPS "src" directory +# and recompile LAMMPS. + + + +import "CGLipidBr2005.lt" + +using namespace CGLipidBr2005 + +# The "= new random" syntax chooses one of several molecules at random + +lipids = new random([DPPC, DLPC], [0.5,0.5], 1234) #"1234"=random_seed + [13].move(7.5, 0, 0) + [15].move(3.75, 6.49519, 0) # <-- hexagonal lattice + [2].rot(180, 1, 0, 0) # <-- 2 monolayers + +# Move all the lipds up to the center of the box + +lipids[*][*][*].move(0,0,75.0) + + + + +# Although this patch of lipids is not square or rectangular, (it looks +# like a parallelogram), this is no longer the case after rectangular +# periodic boundary conditions are applied. (Check by visualising in VMD.) + + +write_once("Data Boundary") { + 0 97.5 xlo xhi + 0 97.42785792 ylo yhi + 0 150.0 zlo zhi +} + + +# A note on geometry: +# We want to create a bilayer arranged in a hexagonal lattice consisting of +# 15 rows (each row is aligned with the x-axis) +# 13 columns (aligned at a 60 degree angle from the x axis) +# The lattice spacing is 7.5 Angstroms. +# When wrapped onto a rectangular box, the dimensions of the system are: +# 13 * 7.5 Angstroms in the X direction +# 15 * 7.5*sqrt(3)/2 Angstroms in the Y direction + + + + + + + +# ------------------- protein inclusion --------------------- + +import "1beadProtSci2010.lt" + +using namespace 1beadProtSci2010 + +protein = new 4HelixInsideOut + +protein.move(45.0, 25.98076211, 75.0) + + +# Delete a hole in the membrane to create space for the protein. + +delete lipids[4][2][*] +delete lipids[6][2][*] +delete lipids[3-6][3][*] +delete lipids[3-5][4][*] +delete lipids[2-5][5][*] +delete lipids[2][6][*] +delete lipids[4][6][*] + +# Note: All atom types must include the full path (the name of +# the namespace which defined them as well as the atom type name). +# (This is because we are no longer inside that namespace.) + + +write_once("In Settings") { + + # ----------------------------------------------------------- + # -------- interactions between protein and lipids ---------- + # ----------------------------------------------------------- + + # Interactions between the protein and lipid atoms are usually + # determined by mixing rules. (However this is not possible some + # for atoms, such as the "int" atoms in the lipid model which + # interact using -1/r^2 attraction.) Mixing rules do not make + # sense for these atoms so we must explicitly define their + # interaction with all other atoms. + + # We want the hydrophobic interactions between hydrophobic residues in + # the protein and beads the interior of the lipid to be energetically + # similar to the attractive interactions between the lipid tails. + # + # Note: I made the width of the outward-facing protein beads slightly larger + # ("12.5") whenever they interact with the "tail" beads in each lipid + # (in order to make the protein wider there). + # This hopefully relieves some of the internal negative pressure in the center + # of the bilayer which can otherwise rip apart the protein or suck it into + # the bilaer. (This is a hack, and I'm not sure if it is necessary. + # For different protein or lipid models, you probably don't need this.) + # + # i j pairstylename eps sig K L + + pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 12.5 0.4 -1 + pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 + + # To help keep the protein from tilting 90 degrees and burying itself + # within the lipid bilayer, we make the turn regions at either + # end of the protein (strongly) attracted to the head groups + # of the lipid. (In reality, they would probably be attracted + # to the water as well.) + + pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 + pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 + + # All other interactions between proteins and lipids are steric. + + pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + + # ----------------------------------------------------------- + # -------- Modifications to the protein model: -------------- + # ----------------------------------------------------------- + # + # Turn off attraction between the hydrophobic "@atom:sH" beads: + # (These beads are located in the outside of a trans-membrane protein.) + + pair_coeff @atom:1beadProtSci2010/sH @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0 + + # (Why: These beads are only attracted to + # each other in an aqueous environment) + + # ... and + # Turn ON attraction between the hydrophilic "@atom:sL" beads. + # (These beads are located in the interior of a trans-membrane protein.) + + pair_coeff @atom:1beadProtSci2010/sL @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 + + # Why? + # In reality, polar groups in the interior of trans-membrane + # proteins do form hydrogen bonds with each other. This was + # absent from the original protein model because, in an aqueous + # environment, these groups preferentially interact with the water. + # + # Why is this necessary? + # Shouldn't attraction between lipid tails and the protein create + # an effective force which brings the hydrophilic beads together? + # (similar to the hydrophobic effect, but in reverse?). + # Answer: + # Unlike an aqueous environment (~zero pressure, or +1atm), there is + # a large negative pressure in the interior of some bilayer membrane + # models (such as this one). Without some kind of direct attraction + # between interior residues, the protein will get pulled apart. + # (Perhaps the attractive force I am using is too strong?) + +} + + + + +# Finally, we must combine the two force-field styles which were used for +# the coarse-grained lipid and protein. To do that, we write one last time +# to the "In Init" section. When reading the "Init" section LAMMPS will +# read these commands last and this will override any earlier settings. + +write_once("In Init") { + # -- These styles override earlier settings -- + units real + atom_style full + # (Hybrid force field styles were used for portability.) + bond_style hybrid harmonic + angle_style hybrid cosine/delta harmonic + dihedral_style hybrid fourier + improper_style none + pair_style hybrid table linear 1130 lj/charmm/coul/charmm/inter es4k4l 14.5 15 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" +} + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/table_int.dat b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/table_int.dat new file mode 100644 index 0000000000..b0d651d67f --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/table_int.dat @@ -0,0 +1,1139 @@ +# Table for the INT-INT interaction from +# Brannigan et al, Phys Rev E, 72, 011915 (2005) +# This table contains +# i r_i U(r_i) -dU/dr|r_i +# where U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) + +INT +N 1130 + +1 0.02 2.0331818401e+30 1.21990910406e+33 +2 0.04 4.9638228518e+26 1.48914685554e+29 +3 0.06 3.82579033251e+24 7.65158066501e+26 +4 0.08 1.21187081343e+23 1.81780622014e+25 +5 0.1 8.32791281704e+21 9.99349538045e+23 +6 0.12 9.34030842897e+20 9.34030842897e+22 +7 0.14 1.46892540453e+20 1.25907891817e+22 +8 0.16 2.95866897809e+19 2.21900173357e+21 +9 0.18 7.19889946863e+18 4.79926631242e+20 +10 0.2 2.0331818401e+18 1.21990910406e+20 +11 0.22 6.47834392264e+17 3.53364213962e+19 +12 0.24 2.28034873754e+17 1.14017436877e+19 +13 0.26 8.72681951932e+16 4.02776285507e+18 +14 0.28 3.58624366341e+16 1.53696157003e+18 +15 0.3 1.56704372019e+16 6.26817488078e+17 +16 0.32 7.2233129348e+15 2.70874235055e+17 +17 0.34 3.48970861422e+15 1.23166186384e+17 +18 0.36 1.75754381558e+15 5.85847938527e+16 +19 0.38 9.18613895646e+14 2.90088598625e+16 +20 0.4 4.96382285179e+14 1.48914685554e+16 +21 0.42 2.76404230108e+14 7.89726371739e+15 +22 0.44 1.58162693423e+14 4.31352800247e+15 +23 0.46 9.27773983256e+13 2.42027995633e+15 +24 0.48 5.56725765996e+13 1.391814415e+15 +25 0.5 3.41111308981e+13 8.18667141564e+14 +26 0.52 2.13057117167e+13 4.91670270393e+14 +27 0.54 1.35459994024e+13 3.0102220895e+14 +28 0.56 8.75547769351e+12 1.87617379153e+14 +29 0.58 5.74645813711e+12 1.18892237325e+14 +30 0.6 3.8257903322e+12 7.65158066491e+13 +31 0.62 2.58128463312e+12 4.99603477424e+13 +32 0.64 1.7635041342e+12 3.30657025205e+13 +33 0.66 1.21901470178e+12 2.21639036726e+13 +34 0.68 8.51979641904e+11 1.50349348607e+13 +35 0.7 6.0167184547e+11 1.0314374497e+13 +36 0.72 4.29087845387e+11 7.15146409276e+12 +37 0.74 3.08855637556e+11 5.00846980094e+12 +38 0.76 2.24270970425e+11 3.54112058818e+12 +39 0.78 1.64210505205e+11 2.52631546702e+12 +40 0.8 1.2118708117e+11 1.81780621971e+12 +41 0.82 90109367359.1 1.31867367068e+12 +42 0.84 67481501334.4 9.64021449503e+11 +43 0.86 50880896383.4 7.09965997788e+11 +44 0.88 38613938681.2 5.26553710913e+11 +45 0.9 29486692086.8 3.93155896009e+11 +46 0.92 22650731882.4 2.95444330322e+11 +47 0.94 17498544395.3 2.23385674464e+11 +48 0.96 13591937526.4 1.69899220331e+11 +49 0.98 10612635712.6 1.29950642555e+11 +50 1.0 8327912706.34 99934953582.6 +51 1.02 6566502316.69 77252969474.2 +52 1.04 5201589672.36 60018343356.8 +53 1.06 4138717434.11 46853405843.3 +54 1.08 3307128665.58 36745874940.0 +55 1.1 2653529579.27 28947596241.1 +56 1.12 2137567708.15 22902511945.9 +57 1.14 1728534024.3 18195095739.0 +58 1.16 1402943799.0 14513212422.1 +59 1.18 1142752163.37 11621209113.9 +60 1.2 934030766.093 9340308300.6 +61 1.22 765981286.774 7534242773.65 +62 1.24 630196371.787 6098675145.29 +63 1.26 520103253.414 4953364870.6 +64 1.28 430542934.103 4036340534.04 +65 1.3 357450462.101 3299543229.91 +66 1.32 297610947.802 2705554551.18 +67 1.34 248472587.186 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(Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# So, after typing "make yes-user-misc" in to the shell, ... +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. +# +# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style" +# then you made a mistake in the instructions above. + + + +# -- Init section -- + +include system.in.init + +# -- Atom definition section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run section -- + +dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz + +minimize 1.0e-5 1.0e-7 500 2000 + +write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.npt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.npt new file mode 100644 index 0000000000..f5f117ece1 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.npt @@ -0,0 +1,60 @@ +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# So, after typing "make yes-user-misc" in to the shell, ... +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. +# +# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style" +# then you made a mistake in the instructions above. +# + +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + +#minimize 1.0e-5 1.0e-7 500 2000 + +timestep 10.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs +dump 1 all custom 10000 traj_npt.lammpstrj id mol type x y z ix iy iz + + +thermo_style custom step temp pe etotal vol epair ebond eangle +thermo 1000 # time interval for printing out "thermo" data + + +fix fxlan all langevin 300.0 300.0 120 48279 +fix fxnph all nph x 0 0 1000 y 0 0 1000 couple xy + + +# Note: The temperature 300.0 K corresponds to 0.907033536873*epsilon +# (for the "epsilon" used by the coarse-grained lipid), and +# to 0.33*epsilon (for the "epsilon" used in the coarse-grained protein) +# Note: The langevin damping parameter "120" corresponds to +# the 0.12ps damping time used in Watson et. al JCP 2011. +# Note: We maintain the system system at constant (zero) tention +# using a barostat damping parameter Pdamp=1000 ("0 0 1000") + + +# optional (not sure if this helps): +# balance x uniform y uniform + + +run 10000000 + +write_restart system_after_npt.rst + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.nvt new file mode 100644 index 0000000000..2ee9ae0199 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.nvt @@ -0,0 +1,67 @@ +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# So, after typing "make yes-user-misc" in to the shell, ... +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. +# +# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style" +# then you made a mistake in the instructions above. +# +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + + +# Normally, I would minimize the system and equilibrate the system at constant +# pressure and temperature beforehand. If you run lammps with "run.in.npt", +# it will generate a restart file "system_after_npt.rst" with reasonable +# coordinates at that temperature and pressure. Then we could load it now: +# +#read_restart system_after_npt.rst +# +# Unfortunately the LAMMPS "read_restart" command has been undependable over +# the past year (2012), and I feel it is safer to remove it from the examples. +# Instead, for this example, I just read the raw coordinates generated by +# moltemplate (and the default volume). (I get fewer questions this way.) +# However you should never run any liquid simulations at constant volume without +# pressure equilibration first. Hopefully in the future "read_restart" will +# work. Until then, try "read_dump", "dump2data.py", or "restart2data". + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + + +timestep 10.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs +dump 1 all custom 10000 traj_nvt.lammpstrj id mol type x y z ix iy iz + + +thermo_style custom step temp pe etotal vol epair ebond eangle +thermo 1000 # time interval for printing out "thermo" data + + +fix fxlan all langevin 300.0 300.0 120 48279 +fix fxnve all nve + +# Note: The energy scale "epsilon" = 2.75kJ/mole = 330.7485200981 Kelvin*kB. +# So a temperature of 300.0 Kelvin corresponds to 0.907033536873*epsilon. +# Note: The langevin damping parameter "120" corresponds to +# the 0.12ps damping time used in Watson et. al JCP 2011. + +#restart 500000 + +run 10000000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README.TXT b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README.TXT new file mode 100644 index 0000000000..295af3fd16 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README.TXT @@ -0,0 +1,33 @@ +Note: + This example may require additional features to be added to LAMMPS. +If LAMMPS complains about an "Invalid pair_style", then copy the code +in the "additional_lammps_code" directory into your LAMMPS "src" directory +and recompile LAMMPS. + +----- Description -------- + +This example contains an implementation of the DPPC lipid bilayer described in: + G. Brannigan, P.F. Philips, and F.L.H. Brown, + Physical Review E, Vol 72, 011915 (2005) +and: + M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown + J. Chem. Phys. 135, 244701 (2011) + +As in Watson(JCP 2011), rigid bond-length constraints +have been replaced by harmonic bonds. + +A truncated version of this lipid (named "DLPC") has also been added. +Unlike the original "DPPC" molecule model, "DLPC" has not been carefully +parameterized to reproduce the correct behavior in a lipid bilayer mixture. + + +------------- + +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_run.sh new file mode 100755 index 0000000000..9598e3b08d --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_run.sh @@ -0,0 +1,33 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The "run.in.nvt" file is a LAMMPS input script containing +# references to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data, and table_int.dat +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.npt # Run a simulation at constant pressure (tension) + +#or + +lmp_linux -i run.in.nvt # Run a simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation are ignored when beginning the simulation at constant volume. +# This can be fixed. Read "run.in.nvt" for equilibration instructions.) + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.npt +#or +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_setup.sh new file mode 100755 index 0000000000..abf2fce64b --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_setup.sh @@ -0,0 +1,28 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # The "table_int.dat" file contains tabular data for the lipid INT-INT atom + # 1/r^2 interaction. We need it too. (This slows down the simulation by x2, + # so I might look for a way to get rid of it later.) + cp -f table_int.dat ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DLPC.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DLPC.jpg new file mode 100644 index 0000000000..637f2f1c7a Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DLPC.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_LR.jpg new file mode 100644 index 0000000000..14f1a1ed2c Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_no_pbc_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_no_pbc_LR.jpg new file mode 100644 index 0000000000..757abe2684 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_no_pbc_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=500ps_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=500ps_LR.jpg new file mode 100644 index 0000000000..2322449c1d Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=500ps_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC.jpg new file mode 100644 index 0000000000..57e093023d Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005Orig.lt b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005Orig.lt new file mode 100644 index 0000000000..c0478f1425 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005Orig.lt @@ -0,0 +1,191 @@ +# Note: +# +# This example may require additional features to be added to LAMMPS. If +# LAMMPS complains about an "Invalid pair_style", then download copy the +# "additional_lammps_code" from moltemplate.org, unpack it into your LAMMPS +# "src" directory and recompile LAMMPS. +# +# -------- Description -------- +# +# This example contains an implementation of the DPPC lipid bilayer described in +# G. Brannigan, P.F. Philips, and F.L.H. Brown, +# Physical Review E, Vol 72, 011915 (2005) +# and: +# M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown +# J. Chem. Phys. 135, 244701 (2011) +# +# As in Watson(JCP 2011), rigid bond-length constraints have been replaced +# by harmonic bonds. +# +# --- DLPC lipids --- +# A truncated version of the DPPC lipid (named "DLPC") has also been added. +# Unlike the original "DPPC" molecule model, "DLPC" has not been carefully +# parameterized to reproduce the correct behavior in a lipid bilayer/mixture. +# (You may need to stiffen the bond-angle forces to make it behave correctly, +# but I did not do this here.) +# +# Units: +# +# The "epsilon" parameter in their model is approximately 2.75 kJ/mole +# ( = 0.657265774378585 kCal/mole, using 1kCal=4.184kJ) +# The "sigma" parameter corresponds to 7.5 angstroms. +# +# +# The new DLPC model is a truncated version of DPPC, +# (Its behaviour has not been rigorously tested.) + + +CGLipidBr2005 { + + + write_once("In Init") { + # -- Default styles for "CGLipidBr2005" -- + units real + atom_style full + # (Hybrid force field styles were used for portability.) + bond_style hybrid harmonic + angle_style hybrid cosine/delta + dihedral_style none + improper_style none + pair_style hybrid table linear 1001 & + lj/charmm/coul/charmm/inter es4k4l 14.5 15 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" + + neighbor 2.0 multi # <- perhaps unnecessary + communicate multi # <- perhaps unnecessary + } + + + DPPC { + write("Data Atoms") { + $atom:h $mol:. @atom:head 0.0 0.00 0.00 33.75 # DPPC head atom + $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 26.25 + $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 18.75 + $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 11.25 + $atom:t3 $mol:. @atom:../tail 0.0 1.00 0.00 3.75 + } + write("Data Bonds") { + $bond:b1 @bond:../backbone $atom:h $atom:i + $bond:b2 @bond:../backbone $atom:i $atom:t1 + $bond:b3 @bond:../backbone $atom:t1 $atom:t2 + $bond:b4 @bond:../backbone $atom:t2 $atom:t3 + } + write("Data Angles") { + $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 + $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 + $angle:a3 @angle:../backbone $atom:t1 $atom:t2 $atom:t3 + } + + # Define properties of the local (lipid-specific) atom:head type atom: + write_once("Data Masses") { + @atom:head 200.0 + } + write_once("In Settings") { + pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + } + + } #DPPC + + + DLPC { + write("Data Atoms") { + $atom:h $mol:. @atom:head 0.0 0.00 0.00 30.00 # DLPC head atom + $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 22.50 + $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 15.00 + $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 7.50 + } + write("Data Bonds") { + $bond:b1 @bond:../backbone $atom:h $atom:i + $bond:b2 @bond:../backbone $atom:i $atom:t1 + $bond:b3 @bond:../backbone $atom:t1 $atom:t2 + } + write("Data Angles") { + $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 + $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 + } + # Define properties of the local (lipid-specific) atom:head type atom: + write_once("Data Masses") { + @atom:head 200.0 + } + write_once("In Settings") { + pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + } + } #DLPC + + + # Particles shared by all lipid types + write_once("Data Masses") { + @atom:int 200.0 + @atom:tail 200.0 + @atom:head 200.0 #<- Default head type. We may override it later. + } + + write_once("In Settings") { + # -- Default settings/parameters for "CGLipidBr2005" -- + # (Hybrid bond & angle styles were used for portability.) + + # As in Watson(JCP 2011), rigid bond-length constraints + # have been replaced by harmonic bonds. + # The k_theta parameter should lie in between 5*epsilon and 10*epsilon. + bond_coeff @bond:backbone harmonic 116.847 7.5 #<--2*5000*eps/sig^2 + } + + write_once("In Settings") { + angle_coeff @angle:backbone cosine/delta 4.60086042 180 #<-- 7*eps + #angle_coeff @angle:backbone cosine/delta 6.57265774 180 #<-- 10*eps + } + + write_once("In Settings") { + + # The interaction of "atom:int" with other "atom:int" atoms is given by + # epsilon*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2), shifted and cutoff at + # r=3*sigma. This was implemented using pair_style table. + # Unfortunately, mixing lj/charmm and "table" pair styles in the same + # simulation is very inneficient. + + pair_coeff @atom:int @atom:int table table_int.dat INT + + # The interaction of tail beads with eachother is given by the formula below + # and with other atoms ...using Lorenz-Berthelot and "repulsive wins" rules: + # epsilon*(0.4*(sigma/r)^12 - 1.0*(sigma/r)^6), + pair_coeff @atom:tail @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 + pair_coeff @atom:int @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 + + # The interaction of head beads which all other beads is given by: + # epsilon*(0.4*(sigma/r)^12 - 0.0*(sigma/r)^6), + + pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + + } # write_once("In Settings") + + # Note: I divided epsilon by 4 to get "0.1643" because we are using the + # "es4k4l" coeffstyle, corresponding to U(r)=eps(4*K*(s/r)^12 + 4*L*(s/r)^6) + # (The "es4k4l" coeffstyle is the default.) Using this convention makes it + # easier to mix this coarse-grained lipid model with other molecular models. + + + +} # CGLipidBr2005 + + + + + + + + +# Note: This example has not been optimized for speed. +# +# Unfortunately, using both lj/charmm and "table" pair styles in the same +# simulation seems to be very inneficient. (The simulation is twice as slow +# as using only the "lj/charmm" pair styles for every pairwise interaction, +# ...and about 25% slower than using "table" for every pairwise interaction. +# However the lennard-jones pair styles support mixing, so we use them to +# make it easier to run these molecules with other molecules which don't use +# pair_table. I felt that portability was worth the extra 25% slow down.) + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py new file mode 100755 index 0000000000..1eb97e6454 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py @@ -0,0 +1,34 @@ +#!/usr/bin/env python + +# Calculate a table of pairwise energies and forces between "INT" atoms +# in the lipid membrane model described in +# Brannigan et al, Phys Rev E, 72, 011915 (2005) +# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) +# However it is truncated at rc2 = 22.5 (shifted upwards to maintain continuity) + +# The previous version included the repulsive core term +def U(r, eps, sigma): + return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) +def F(r, eps, sigma): + return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) +# We don't want to do that. Instead compute the core repulsion using a +# different pair_style and add the attractive term on top of it using the table. +# This way it the core repulsion acts as a default interaction with other atom +# types (using the new repulsive mixing rules). + +epsilon = 2.75/4.184 # kCal/mole +sigma = 7.5 +Rmin = 0.02 +Rmax = 22.6 +rcut = 22.5 +N = 1130 + +for i in range(0,N): + r = Rmin + i*(Rmax-Rmin)/(N-1) + U_r = U(r, epsilon, sigma) - U(rcut, epsilon, sigma) + F_r = F(r, epsilon, sigma) + if r > rcut: + U_r = 0.0 + F_r = 0.0 + print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py new file mode 100755 index 0000000000..32147e444a --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py @@ -0,0 +1,70 @@ +#!/usr/bin/env python + +# Calculate a table of pairwise energies and forces between "INT" atoms +# in the lipid membrane model described in +# Brannigan et al, Phys Rev E, 72, 011915 (2005) +# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) +# I realized later this is not what we want because although energy is conserved +# all enrgies are shifted with respect to energies used in the Brannigan paper +# (by 0.27 kCal/mole) and the later Watson JCP 2011 paper (by 0.224 kCal/mole). +# (So don't use this.) + +# Calculate and print a + +def S(r, rc1, rc2, derivative=False): + """ + Calculate the switching function S(r) which decays continuously + between 1 and 0 in the range from rc1 to rc2 (rc2>rc1): + S(r) = (rc2^2 - r^2)^2 * (rc2^2 + 2*r^2 - 3*rc1^2) / (rc2^2-rc1^2)^3 + I'm using the same smoothing/switching cutoff function used by the CHARMM + force-fields. (I'm even using the same code to implement it, taken + from lammps charmm/coul/charmm pair style, rewritten in python.) + + """ + assert(rc2>rc1) + rsq = r*r + rc1sq = rc1*rc1 + rc2sq = rc2*rc2 + denom_lj_inv = (1.0 / ((rc2sq-rc1sq)* + (rc2sq-rc1sq)* + (rc2sq-rc1sq))) + if rsq > rc2sq: + return 0.0 + elif rsq < rc1sq: + if derivative: + return 0.0 + else: + return 1.0 + else: + rc2sq_minus_rsq = (rc2sq - rsq) + rc2sq_minus_rsq_sq = rc2sq_minus_rsq * rc2sq_minus_rsq + if derivative: + return (12.0 * rsq * rc2sq_minus_rsq * (rsq-rc1sq) * denom_lj_inv) + else: + return (rc2sq_minus_rsq_sq * + (rc2sq + 2.0*rsq - 3.0*rc1sq) * denom_lj_inv) + + +def U(r, eps, sigma): + return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) + +def F(r, eps, sigma): + return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) + +epsilon = 2.75/4.184 # kCal/mole +sigma = 7.5 +Rmin = 0.02 +Rmax = 22.6 +Rc1 = 22.0 +Rc2 = 22.5 +N = 1130 + +for i in range(0,N): + r = Rmin + i*(Rmax-Rmin)/(N-1) + U_r = U(r, epsilon, sigma) + F_r = F(r, epsilon, sigma) + # Multiply U(r) & F(r) by the smoothing/switch function + U_r = U_r * S(r, Rc1, Rc2) + F_r = U_r * S(r, Rc1, Rc2, True) + F_r * S(r, Rc1, Rc2, False) + print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/system.lt new file mode 100644 index 0000000000..c556233c0d --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/system.lt @@ -0,0 +1,94 @@ +# Description: + +# This constructs a bilayer constructed from coarse-grained DPPC lipids +# (implicit solvent). The DPPC lipid model is described here: +# G. Brannigan, P.F. Philips, and F.L.H. Brown, +# Physical Review E, Vol 72, 011915 (2005) +# +# NOTE: There is an example of a 50%/50% DPPC & DLPC mixture +# in the "membrane+protein" and "vesicle" examples. + + + + + + +import "CGLipidBr2005Orig.lt" + +using namespace CGLipidBr2005 + +lipids = new DPPC [32].move(7.5, 0, 0) + [37].move(3.75, 6.49519, 0) + [2].rot(180, 1, 0, 0) + + +# Move the lipds up to the center of the box +lipids[*][*][*].move(0,0,75.0) + + +# Although this patch of lipids is not square or rectangular, (it looks +# like a parallelogram), this is no longer the case after rectangular +# periodic boundary conditions are applied. We apply them below: +# width: 240 = 32*7.5 +# height: 240.322 = 37*6.49519 + +write_once("Data Boundary") { + 0 240 xlo xhi + 0 240.322 ylo yhi + 0 150.0 zlo zhi +} + + + + + + + + +# -------------- File ends here. Only comments below.------------------- + +# ------------------------------------ +# ------------- COMMENTS: ------------ +# ------------------------------------ +# +# A note on geometry: +# We want to create a bilayer arranged in a hexagonal lattice consisting of +# 32 rows (each row is aligned with the x-axis) +# 37 columns (aligned at a 60 degree angle from the x axis) +# The lattice spacing is 8.0 Angstroms ( ~= 0.95*sigma*2^(1/6), where sigma=7.5) +# When wrapped onto a rectangular box, the dimensions of the system are: +# 32 * 7.5 Angstroms in the X direction +# 37 * 7.5*sqrt(3)/2 Angstroms in the Y direction +# ------------------------------------ +# +# Below I show simple ways to create a lipid bilayer: +# +# 1) If you just want to make lipid bilayer out of DPPC, +# without specifying the location of each lipid, you could use this syntax: +# lipids = new DPPC [32][37][2] # 3-D array +# Later you can load in the coordinates of the lipds from a PDB file. +# Alternately you could also use a 1-dimensional array: +# lipids = new DPPC [2368] # 1-D array. Note: 2368 = 32 x 37 x 2 +# It does not matter as long as the number of lipids is correct. +# Multidimensional arrays are only useful if you plan to apply independent +# coordinate transformations to each row and column and monolayer. See below: +# +# 2) Instead of loading a PDB file later, we can directly specify the location +# of each DPPC lipid in the LT file itself. For lipid bilayers, this is +# easy, because the bilayer structure resembles 2 planar lattices. +# We can use "move" commands to place each lipid, and the "rot" command +# to turn the lipids in one of the monolayers upside down. +# +# lipids = new DPPC [32].move(7.5, 0, 0) +# [37].move(3.75, 6.49519, 0) +# [2].rot(180, 1, 0, 0) +# +# 3) If you want to create a bilayer from a mixture of DPPC and DLPC, you must +# replace "DPPC" in the command above with random([DPPC,DLPC],[0.5,0.5],12345) +# Here "0.5,0.5" are the probabilities for each molecule type, and "12345" +# is an optional random seed. +# lipids = new random([DPPC,DLPC], [0.5,0.5], 12345) +# [32].move(7.5, 0, 0) +# [37].move(3.75, 6.49519, 0) +# [2].rot(180, 1, 0, 0) +# diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/table_int.dat b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/table_int.dat new file mode 100644 index 0000000000..b0d651d67f --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/table_int.dat @@ -0,0 +1,1139 @@ +# Table for the INT-INT interaction from +# Brannigan et al, Phys Rev E, 72, 011915 (2005) +# This table contains +# i r_i U(r_i) -dU/dr|r_i +# where U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) + +INT +N 1130 + +1 0.02 2.0331818401e+30 1.21990910406e+33 +2 0.04 4.9638228518e+26 1.48914685554e+29 +3 0.06 3.82579033251e+24 7.65158066501e+26 +4 0.08 1.21187081343e+23 1.81780622014e+25 +5 0.1 8.32791281704e+21 9.99349538045e+23 +6 0.12 9.34030842897e+20 9.34030842897e+22 +7 0.14 1.46892540453e+20 1.25907891817e+22 +8 0.16 2.95866897809e+19 2.21900173357e+21 +9 0.18 7.19889946863e+18 4.79926631242e+20 +10 0.2 2.0331818401e+18 1.21990910406e+20 +11 0.22 6.47834392264e+17 3.53364213962e+19 +12 0.24 2.28034873754e+17 1.14017436877e+19 +13 0.26 8.72681951932e+16 4.02776285507e+18 +14 0.28 3.58624366341e+16 1.53696157003e+18 +15 0.3 1.56704372019e+16 6.26817488078e+17 +16 0.32 7.2233129348e+15 2.70874235055e+17 +17 0.34 3.48970861422e+15 1.23166186384e+17 +18 0.36 1.75754381558e+15 5.85847938527e+16 +19 0.38 9.18613895646e+14 2.90088598625e+16 +20 0.4 4.96382285179e+14 1.48914685554e+16 +21 0.42 2.76404230108e+14 7.89726371739e+15 +22 0.44 1.58162693423e+14 4.31352800247e+15 +23 0.46 9.27773983256e+13 2.42027995633e+15 +24 0.48 5.56725765996e+13 1.391814415e+15 +25 0.5 3.41111308981e+13 8.18667141564e+14 +26 0.52 2.13057117167e+13 4.91670270393e+14 +27 0.54 1.35459994024e+13 3.0102220895e+14 +28 0.56 8.75547769351e+12 1.87617379153e+14 +29 0.58 5.74645813711e+12 1.18892237325e+14 +30 0.6 3.8257903322e+12 7.65158066491e+13 +31 0.62 2.58128463312e+12 4.99603477424e+13 +32 0.64 1.7635041342e+12 3.30657025205e+13 +33 0.66 1.21901470178e+12 2.21639036726e+13 +34 0.68 8.51979641904e+11 1.50349348607e+13 +35 0.7 6.0167184547e+11 1.0314374497e+13 +36 0.72 4.29087845387e+11 7.15146409276e+12 +37 0.74 3.08855637556e+11 5.00846980094e+12 +38 0.76 2.24270970425e+11 3.54112058818e+12 +39 0.78 1.64210505205e+11 2.52631546702e+12 +40 0.8 1.2118708117e+11 1.81780621971e+12 +41 0.82 90109367359.1 1.31867367068e+12 +42 0.84 67481501334.4 9.64021449503e+11 +43 0.86 50880896383.4 7.09965997788e+11 +44 0.88 38613938681.2 5.26553710913e+11 +45 0.9 29486692086.8 3.93155896009e+11 +46 0.92 22650731882.4 2.95444330322e+11 +47 0.94 17498544395.3 2.23385674464e+11 +48 0.96 13591937526.4 1.69899220331e+11 +49 0.98 10612635712.6 1.29950642555e+11 +50 1.0 8327912706.34 99934953582.6 +51 1.02 6566502316.69 77252969474.2 +52 1.04 5201589672.36 60018343356.8 +53 1.06 4138717434.11 46853405843.3 +54 1.08 3307128665.58 36745874940.0 +55 1.1 2653529579.27 28947596241.1 +56 1.12 2137567708.15 22902511945.9 +57 1.14 1728534024.3 18195095739.0 +58 1.16 1402943799.0 14513212422.1 +59 1.18 1142752163.37 11621209113.9 +60 1.2 934030766.093 9340308300.6 +61 1.22 765981286.774 7534242773.65 +62 1.24 630196371.787 6098675145.29 +63 1.26 520103253.414 4953364870.6 +64 1.28 430542934.103 4036340534.04 +65 1.3 357450462.101 3299543229.91 +66 1.32 297610947.802 2705554551.18 +67 1.34 248472587.186 2225128105.44 +68 1.36 208002782.573 1835319108.76 +69 1.38 174576985.011 1518061159.35 +70 1.4 146892484.084 1259078837.33 +71 1.42 123901294.937 1047053582.16 +72 1.44 104757721.536 872981382.419 +73 1.46 88777241.639 729676313.267 +74 1.48 75404158.02 611385405.387 +75 1.5 64186061.7033 513488820.507 +76 1.52 54753607.1486 432265633.695 +77 1.54 46804443.7318 364710253.134 +78 1.56 40090410.0598 308388060.159 +79 1.58 34407297.9713 261321529.95 +80 1.6 29586646.6744 221900119.2 +81 1.62 25489145.661 188808745.634 +82 1.64 21999316.2868 160970856.824 +83 1.66 19021212.5921 137502982.517 +84 1.68 16474936.8715 117678352.86 +85 1.7 14293808.3245 100897694.735 +86 1.72 12422056.6082 86665727.6626 +87 1.74 10812938.3788 74572197.8496 +88 1.76 9427195.57103 64276535.39 +89 1.78 8231790.46096 55495411.7777 +90 1.8 7198865.45512 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b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.min @@ -0,0 +1,28 @@ +# -- Init section -- + +include system.in.init + +# -- Atom definition section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# Optional: Make sure the pairwise energies look reasonable: +#pair_write 2 2 1001 r 2.6 16.0 test_tail-tail.dat t-t 0 0 +#pair_write 2 3 1001 r 2.6 16.0 test_tail-head.dat t-h 0 0 +#pair_write 1 2 1001 r 2.6 16.0 test_int-tail.dat i-t 0 0 +#pair_write 1 1 2573 r 2.6 16.0 test_int-int.dat i-i 0 0 +#pair_write 1 3 1001 r 2.6 16.0 test_int-head.dat i-h 0 0 +#pair_write 3 3 1001 r 2.6 16.0 test_head-head.dat h-h 0 0 + + +# -- Run section -- + +dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz + +minimize 1.0e-5 1.0e-7 500 2000 + +write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.npt b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.npt new file mode 100644 index 0000000000..bd86869ab7 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.npt @@ -0,0 +1,57 @@ +# -------- REQUIREMENTS: --------- +# 1) This example may require additional features and bug fixes for LAMMPS. +# Be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 2) Unpack it +# 3) copy the .cpp and .h files to the src folding of your lammps installation. +# 4) Compile LAMMPS. +# +# (If LAMMPS complains about an "Invalid pair_style" +# then you made a mistake in the instructions above.) +# + +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 6.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs +dump 1 all custom 5000 traj_npt.lammpstrj id mol type x y z ix iy iz + + +thermo_style custom step temp pe etotal vol epair ebond eangle +thermo 1000 # time interval for printing out "thermo" data + + +fix fxlan all langevin 300.0 300.0 120 48279 +fix fxnph all nph x 0 0 1000 y 0 0 1000 couple xy + + +# Note: The temperature 300.0 K corresponds to 0.907033536873*epsilon +# for the "epsilon" used by the coarse-grained lipid. +# Note: The langevin damping parameter "120" corresponds to +# the 0.12ps damping time used in Watson et. al JCP 2011. +# Note: We maintain the system system at constant (zero) tention +# using a barostat damping parameter Pdamp=1000 ("0 0 1000") + + +# optional (not sure if this helps): +# balance x uniform y uniform + + +#restart 1000000 + +run 2000000 + +write_restart system_after_npt.rst + diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.nvt new file mode 100644 index 0000000000..775c074c21 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.nvt @@ -0,0 +1,53 @@ +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + + +# Normally, I would minimize the system and equilibrate the system at constant +# pressure and temperature beforehand. If you run lammps with "run.in.npt", +# it will generate a restart file "system_after_npt.rst" with reasonable +# coordinates at that temperature and pressure. Then we could load it now: +# +#read_restart system_after_npt.rst +# +# Unfortunately the LAMMPS "read_restart" command has been undependable over +# the past year (2012), and I feel it is safer to remove it from the examples. +# Instead, for this example, I just read the raw coordinates generated by +# moltemplate (and the default volume). (I get fewer questions this way.) +# However you should never run any liquid simulations at constant volume without +# pressure equilibration first. Hopefully in the future "read_restart" will +# work. Until then, try "read_dump", "dump2data.py", or "restart2data". + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + + +timestep 6.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs +dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz + + +thermo_style custom step temp pe etotal vol epair ebond eangle +thermo 1000 # time interval for printing out "thermo" data + + +fix fxlan all langevin 300.0 300.0 120 48279 +fix fxnve all nve + +# Note: The energy scale "epsilon" = 2.75kJ/mole = 330.7485200981 Kelvin*kB. +# So a temperature of 300.0 Kelvin corresponds to 0.907033536873*epsilon. +# Note: The langevin damping parameter "120" corresponds to +# the 0.12ps damping time used in Watson et. al JCP 2011. + +#restart 1000000 + +run 1000000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/README.TXT new file mode 100644 index 0000000000..31abcd66ef --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/README.TXT @@ -0,0 +1,33 @@ +# This directory contains examples of how to run a short simulation of a +# coarse-grained protein-like polymer, folding in the presence and absence of +# a chaperone (modeled as an attractive or repulsie spherical shell). +# +# The protein models and the chaperone models are described and used here: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) +# ...and also here: +# AI Jewett and J-E Shea, J. Mol. Biol, Vol 363(5), (2006) +# +# (In the "frustrated+minichaperone" directory, the protein is +# placed outside the chaperone sphere, as opposed to inside.) +# +# -------- REQUIREMENTS: --------- +# 1) These examples require the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) They also may require additional features and bug fixes for LAMMPS. +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. +# + +------------- +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files in each directory. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README.TXT new file mode 100644 index 0000000000..a52f73ff7b --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README.TXT @@ -0,0 +1,32 @@ +# This directory demonstrates how to run a long simulation of +# the "frustrated" coarse-grained protein confined in a frustrated +# coarse-grained chaperonin (R=6, h=0.475) as described in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) +# +# Note: If you want to use a "hydrophilic" chaperone (with h=0.0 +# instead of h=0.475), then replace the word "CHAP_INTERIOR_H0.475" +# (at the end of "system.lt") with "CHAP_INTERIOR_H0" +# +# Because this process takes a long time (even with the help of the chaperone) +# I save the data relatively infrequently. +# +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. + +------------- +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh new file mode 100755 index 0000000000..45bd2d451d --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh @@ -0,0 +1,31 @@ +# You would probably run lammps this way: +# +# lmp_ubuntu -i run.in.nvt + +# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer +# to the input scripts & data files you created earlier when you ran moltemplate +# system.in.init, system.in.settings, system.data + + + + +# ----------------------------------- + + + +LAMMPS_COMMAND="lmp_ubuntu" + +# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps +# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. + +# Run lammps using the following 3 commands: + +"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +"$LAMMPS_COMMAND" -i run.in.nvt # production run + +# Alternately, if you have MPI installed, try something like this: + +#NUMPROCS=4 +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_setup.sh new file mode 100755 index 0000000000..f2462426f1 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_setup.sh @@ -0,0 +1,24 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -overlay-dihdedrals system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + cp -r table*.dat ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 0000000000..9e34246f8e --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,86 @@ +PSF + + 1 !NTITLE + REMARKS VMD generated structure x-plor psf file + + 28 !NATOM + 1 1 2 2 0.000000 1.0000 0 + 2 1 1 1 0.000000 1.0000 0 + 3 1 2 2 0.000000 1.0000 0 + 4 1 1 1 0.000000 1.0000 0 + 5 1 2 2 0.000000 1.0000 0 + 6 1 1 1 0.000000 1.0000 0 + 7 1 3 3 0.000000 1.0000 0 + 8 1 3 3 0.000000 1.0000 0 + 9 1 1 1 0.000000 1.0000 0 + 10 1 2 2 0.000000 1.0000 0 + 11 1 1 1 0.000000 1.0000 0 + 12 1 2 2 0.000000 1.0000 0 + 13 1 1 1 0.000000 1.0000 0 + 14 1 2 2 0.000000 1.0000 0 + 15 1 3 3 0.000000 1.0000 0 + 16 1 3 3 0.000000 1.0000 0 + 17 1 3 3 0.000000 1.0000 0 + 18 1 1 1 0.000000 1.0000 0 + 19 1 1 1 0.000000 1.0000 0 + 20 1 2 2 0.000000 1.0000 0 + 21 1 2 2 0.000000 1.0000 0 + 22 1 1 1 0.000000 1.0000 0 + 23 1 1 1 0.000000 1.0000 0 + 24 1 2 2 0.000000 1.0000 0 + 25 1 2 2 0.000000 1.0000 0 + 26 1 1 1 0.000000 1.0000 0 + 27 1 2 2 0.000000 1.0000 0 + 28 2 4 4 0.000000 100.0000 0 + + 26 !NBOND: bonds + 1 2 2 3 3 4 4 5 + 5 6 6 7 7 8 8 9 + 9 10 10 11 11 12 12 13 + 13 14 14 15 15 16 16 17 + 17 18 18 19 19 20 20 21 + 21 22 22 23 23 24 24 25 + 25 26 26 27 + + 25 !NTHETA: angles + 13 14 15 7 8 9 6 7 8 + 16 17 18 15 16 17 2 3 4 + 4 5 6 9 10 11 11 12 13 + 14 15 16 1 2 3 3 4 5 + 10 11 12 12 13 14 25 26 27 + 5 6 7 8 9 10 17 18 19 + 18 19 20 22 23 24 21 22 23 + 19 20 21 20 21 22 23 24 25 + 24 25 26 + + 19 !NPHI: dihedrals + 1 2 3 4 2 3 4 5 + 3 4 5 6 4 5 6 7 + 8 9 10 11 9 10 11 12 + 10 11 12 13 11 12 13 14 + 12 13 14 15 15 16 17 18 + 16 17 18 19 17 18 19 20 + 18 19 20 21 19 20 21 22 + 20 21 22 23 21 22 23 24 + 22 23 24 25 23 24 25 26 + 24 25 26 27 + + 0 !NIMPHI: impropers + + + 0 !NDON: donors + + + 0 !NACC: acceptors + + + 0 !NNB + + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 + + 1 0 !NGRP + 0 0 0 + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/misfolded+chaperonin_t=0tau_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/misfolded+chaperonin_t=0tau_LR.jpg new file mode 100644 index 0000000000..31853cd5ad Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/misfolded+chaperonin_t=0tau_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/unfolded+chaperonin_t=508750tau_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/unfolded+chaperonin_t=508750tau_LR.jpg new file mode 100644 index 0000000000..fdc5c890b1 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/unfolded+chaperonin_t=508750tau_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated.lt new file mode 100644 index 0000000000..e43026ba9f --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated.lt @@ -0,0 +1,216 @@ +# This file defines the "frustrated" coarse-grained protein model used in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) + + +1beadFrustrated { + + # There are 3 atom types (referred to above as B, L, and N) + # Define their masses: + + write_once("Data Masses") { + @atom:B 1.0 + @atom:L 1.0 + @atom:N 1.0 + } + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol @atom:L 0.0 -0.92636654 -1.8409904 -2.1482679 + $atom:a2 $mol @atom:B 0.0 -0.57313354 -1.0670787 -1.6182341 + $atom:a3 $mol @atom:L 0.0 -0.85707399 -1.2358703 -0.69350966 + $atom:a4 $mol @atom:B 0.0 -0.44231274 -0.4584993 -0.23418709 + $atom:a5 $mol @atom:L 0.0 -0.75081182 -0.62868078 0.69786737 + $atom:a6 $mol @atom:B 0.0 -0.36201977 0.11619615 1.2249098 + $atom:a7 $mol @atom:N 0.0 -0.63708237 -0.15973084 2.1723919 + $atom:a8 $mol @atom:N 0.0 0.20516047 0.10417157 2.624901 + $atom:a9 $mol @atom:B 0.0 0.57223743 0.44728103 1.7695617 + $atom:a10 $mol @atom:L 0.0 0.77646279 -0.40630393 1.3168043 + $atom:a11 $mol @atom:B 0.0 0.45475664 -0.2077937 0.40045721 + $atom:a12 $mol @atom:L 0.0 0.72712495 -1.0397637 -0.087614951 + $atom:a13 $mol @atom:B 0.0 0.36971183 -0.85840501 -0.9933019 + $atom:a14 $mol @atom:L 0.0 0.74784336 -1.5700415 -1.5859217 + $atom:a15 $mol @atom:N 0.0 0.43423905 -1.2758917 -2.4853429 + $atom:a16 $mol @atom:N 0.0 0.70583191 -0.30726921 -2.4987711 + $atom:a17 $mol @atom:N 0.0 -0.091688915 0.23323014 -2.2051358 + $atom:a18 $mol @atom:B 0.0 -0.34243283 -0.035822049 -1.2644719 + $atom:a19 $mol @atom:B 0.0 0.41961247 0.18475451 -0.65971014 + $atom:a20 $mol @atom:L 0.0 0.51968465 1.1546791 -0.77877053 + $atom:a21 $mol @atom:L 0.0 -0.40827985 1.2765273 -0.52550748 + $atom:a22 $mol @atom:B 0.0 -0.368141 0.58090904 0.19152224 + $atom:a23 $mol @atom:B 0.0 0.40327249 0.86101769 0.7336255 + $atom:a24 $mol @atom:L 0.0 0.22707289 1.8326235 0.89673346 + $atom:a25 $mol @atom:L 0.0 -0.66500182 1.7285809 1.2783166 + $atom:a26 $mol @atom:B 0.0 -0.39205603 1.0475436 1.9328097 + $atom:a27 $mol @atom:L 0.0 0.25339027 1.5246265 2.5388463 + } + + # bond-ID bond-Type atom-ID atom-ID + + write('Data Bonds') { + $bond:b1 @bond:backbone $atom:a1 $atom:a2 + $bond:b2 @bond:backbone $atom:a2 $atom:a3 + $bond:b3 @bond:backbone $atom:a3 $atom:a4 + $bond:b4 @bond:backbone $atom:a4 $atom:a5 + $bond:b5 @bond:backbone $atom:a5 $atom:a6 + $bond:b6 @bond:backbone $atom:a6 $atom:a7 + $bond:b7 @bond:backbone $atom:a7 $atom:a8 + $bond:b8 @bond:backbone $atom:a8 $atom:a9 + $bond:b9 @bond:backbone $atom:a9 $atom:a10 + $bond:b10 @bond:backbone $atom:a10 $atom:a11 + $bond:b11 @bond:backbone $atom:a11 $atom:a12 + $bond:b12 @bond:backbone $atom:a12 $atom:a13 + $bond:b13 @bond:backbone $atom:a13 $atom:a14 + $bond:b14 @bond:backbone $atom:a14 $atom:a15 + $bond:b15 @bond:backbone $atom:a15 $atom:a16 + $bond:b16 @bond:backbone $atom:a16 $atom:a17 + $bond:b17 @bond:backbone $atom:a17 $atom:a18 + $bond:b18 @bond:backbone $atom:a18 $atom:a19 + $bond:b19 @bond:backbone $atom:a19 $atom:a20 + $bond:b20 @bond:backbone $atom:a20 $atom:a21 + $bond:b21 @bond:backbone $atom:a21 $atom:a22 + $bond:b22 @bond:backbone $atom:a22 $atom:a23 + $bond:b23 @bond:backbone $atom:a23 $atom:a24 + $bond:b24 @bond:backbone $atom:a24 $atom:a25 + $bond:b25 @bond:backbone $atom:a25 $atom:a26 + $bond:b26 @bond:backbone $atom:a26 $atom:a27 + } + + # (3-body) Angles are specified below + + # (4-body) Dihedrals must be defined explicitly for every quartet of atoms. + # (These interactions are not determined by atom type.) + + # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID + + write('Data Dihedrals') { + + $dihedral:d1 @dihedral:beta $atom:a1 $atom:a2 $atom:a3 $atom:a4 + $dihedral:d2 @dihedral:beta $atom:a2 $atom:a3 $atom:a4 $atom:a5 + $dihedral:d3 @dihedral:beta $atom:a3 $atom:a4 $atom:a5 $atom:a6 + $dihedral:d4 @dihedral:beta $atom:a4 $atom:a5 $atom:a6 $atom:a7 + + # Dihedral angle forces in the turn regions were switched off + # (in this model) so just I comment them out (and \ the variable names). + # \$dihedral:d5 \@dihedral:turn $atom:a5 $atom:a6 $atom:a7 $atom:a8 + # \$dihedral:d6 \@dihedral:turn $atom:a6 $atom:a7 $atom:a8 $atom:a9 + # \$dihedral:d7 \@dihedral:turn $atom:a7 $atom:a8 $atom:a9 $atom:a10 + + $dihedral:d8 @dihedral:beta $atom:a8 $atom:a9 $atom:a10 $atom:a11 + $dihedral:d9 @dihedral:beta $atom:a9 $atom:a10 $atom:a11 $atom:a12 + $dihedral:d10 @dihedral:beta $atom:a10 $atom:a11 $atom:a12 $atom:a13 + $dihedral:d11 @dihedral:beta $atom:a11 $atom:a12 $atom:a13 $atom:a14 + $dihedral:d12 @dihedral:beta $atom:a12 $atom:a13 $atom:a14 $atom:a15 + + # Dihedral angle forces in the turn regions were switched off + # (in this model) so just I comment them out (and \ the variable names). + # \$dihedral:d13 \@dihedral:turn $atom:a13 $atom:a14 $atom:a15 $atom:a16 + # \$dihedral:d14 \@dihedral:turn $atom:a14 $atom:a15 $atom:a16 $atom:a17 + + $dihedral:d15 @dihedral:alpha $atom:a15 $atom:a16 $atom:a17 $atom:a18 + $dihedral:d16 @dihedral:alpha $atom:a16 $atom:a17 $atom:a18 $atom:a19 + $dihedral:d17 @dihedral:alpha $atom:a17 $atom:a18 $atom:a19 $atom:a20 + $dihedral:d18 @dihedral:alpha $atom:a18 $atom:a19 $atom:a20 $atom:a21 + $dihedral:d19 @dihedral:alpha $atom:a19 $atom:a20 $atom:a21 $atom:a22 + $dihedral:d20 @dihedral:alpha $atom:a20 $atom:a21 $atom:a22 $atom:a23 + $dihedral:d21 @dihedral:alpha $atom:a21 $atom:a22 $atom:a23 $atom:a24 + $dihedral:d22 @dihedral:alpha $atom:a22 $atom:a23 $atom:a24 $atom:a25 + $dihedral:d23 @dihedral:alpha $atom:a23 $atom:a24 $atom:a25 $atom:a26 + $dihedral:d24 @dihedral:alpha $atom:a24 $atom:a25 $atom:a26 $atom:a27 + } + + # All consecutively bonded triplets of atoms same 3-body bond-angle + # interaction parameters. Of coarse, we could specify them all explicitly + # (as we did for the dihedrals above), but I wanted to show how to specify + # angles by atom type instead. (You can do this for dihedrals & impropers + # also.) + + # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type + + write_once('Data Angles By Type') { + @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* + } + + # (The "*" is a wildcard character. I use "*" to denote any atom-type or + # bond-type which is defined within the current namespace: 1beadFrustrated) + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 + pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0 + pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0 + pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1 + pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0 + pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0 + } + + + # 2-body (bonded) interactions: + # + # Ubond(r) = (k/2)*(r-0)^2 + # + # The corresponding command is: + # + # bond-Type bondstylename k r0 + + write_once("In Settings") { + bond_coeff @bond:backbone harmonic 100.0 1.0 + } + + # 3-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Uangle(theta) = (k/2)*(theta-theta0)^2 + # (k in kcal/mol/rad^2, theta0 in degrees) + # + # angle-Type anglestylename k theta0 + + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 13.3333333333 105.0 + } + + + # We use tabular dihedral potentials to implement the dihedral forces. + # (Actually there is a way to use Fourier series, using multiple charmm + # style dihedral interactions, but it's slower and messier.) + + write_once("In Settings") { + # style file keyword + dihedral_coeff @dihedral:alpha table table_dihedral_frustrated.dat FRUSTRATED_ALPHA + dihedral_coeff @dihedral:beta table table_dihedral_frustrated.dat FRUSTRATED_BETA + # No need to specify dihedral interactions in the turn regions. (none exist) + } + + write_once("In Settings") { + # Optional: define the atoms in the "proteins" group + group proteins type @atom:B + group proteins type @atom:L + group proteins type @atom:N + } + + # LAMMPS has many available force field styles (and atom styles). + # Here, we pick the ones which work well for this molecular model: + + write_once("In Init") { + # --- Default options for the "1BeadFrustrated" protein model --- + # --- (These can be overridden later.) --- + units lj + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid table spline 360 + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + +} # 1beadFrustrated + + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated_variants.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated_variants.lt new file mode 100644 index 0000000000..54e2de4376 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated_variants.lt @@ -0,0 +1,85 @@ +import "1beadFrustrated.lt" + + +# Alternate starting conformation (same molecule): + + +1beadMisfolded inherits 1beadFrustrated { + + # This molecule "inherits" all of its features from "1beadFrustrated". + # Here we override the atomic positions with new coordinates: + + # AtomID MoleculeID AtomType Charge X Y Z + + write("Data Atoms") { + $atom:a1 $mol @atom:L 0.0 -0.69801399 -0.22114168 -1.9464876 + $atom:a2 $mol @atom:B 0.0 -0.40921658 -0.027063664 -1.0033251 + $atom:a3 $mol @atom:L 0.0 0.10259348 0.80836418 -1.0737085 + $atom:a4 $mol @atom:B 0.0 0.25857916 1.0054984 -0.11621451 + $atom:a5 $mol @atom:L 0.0 0.8258629 1.8325549 -0.18529135 + $atom:a6 $mol @atom:B 0.0 0.91366257 2.1950317 0.74175977 + $atom:a7 $mol @atom:N 0.0 1.4399539 1.554238 1.2994409 + $atom:a8 $mol @atom:N 0.0 0.73372573 1.0161012 1.7397275 + $atom:a9 $mol @atom:B 0.0 0.26608782 0.65302497 0.94353938 + $atom:a10 $mol @atom:L 0.0 0.97442305 0.13574211 0.50586398 + $atom:a11 $mol @atom:B 0.0 0.35889617 -0.18247555 -0.1764186 + $atom:a12 $mol @atom:L 0.0 0.87151735 -0.77260824 -0.75240916 + $atom:a13 $mol @atom:B 0.0 0.047726486 -1.0530682 -1.1902704 + $atom:a14 $mol @atom:L 0.0 0.34530697 -1.7476773 -1.8393331 + $atom:a15 $mol @atom:N 0.0 0.65865186 -2.45948 -1.2167056 + $atom:a16 $mol @atom:N 0.0 -0.16534524 -2.6219442 -0.67112167 + $atom:a17 $mol @atom:N 0.0 -0.010590421 -2.2445242 0.24748633 + $atom:a18 $mol @atom:B 0.0 0.18135771 -1.2564919 0.1767523 + $atom:a19 $mol @atom:B 0.0 -0.57472665 -0.82852797 -0.27027791 + $atom:a20 $mol @atom:L 0.0 -1.3967448 -1.0516787 0.24247346 + $atom:a21 $mol @atom:L 0.0 -1.003428 -0.85642681 1.1107555 + $atom:a22 $mol @atom:B 0.0 -0.25156735 -0.3182346 0.74262946 + $atom:a23 $mol @atom:B 0.0 -0.61751956 0.30115562 0.070426493 + $atom:a24 $mol @atom:L 0.0 -1.3347934 0.83310182 0.52625934 + $atom:a25 $mol @atom:L 0.0 -0.83315257 1.270904 1.2564086 + $atom:a26 $mol @atom:B 0.0 -0.10469759 1.6988523 0.72597181 + $atom:a27 $mol @atom:L 0.0 -0.57854905 2.3367737 0.11206868 + } + +} # 1beadMisfolded + + +1beadUnfolded inherits 1beadFrustrated { + + # This molecule "inherits" all of its features from "1beadFrustrated" + # Here we override the atomic positions with new coordinates: + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0 + $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8 + $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8 + $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0 + $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0 + $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8 + $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8 + $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0 + $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0 + $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8 + $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8 + $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0 + $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0 + $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8 + $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8 + $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2 + $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2 + $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6 + $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6 + $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2 + $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2 + $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6 + $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6 + $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2 + $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2 + $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6 + $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6 + } + +} # 1beadUnfolded + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/chaperonin.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/chaperonin.lt new file mode 100644 index 0000000000..8266d2a898 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/chaperonin.lt @@ -0,0 +1,41 @@ +# Here we define a trivial molecule containing only one particle. + +Chaperonin { + + # atomID molID atomType charge x y z + + write("Data Atoms") { + $atom:C $mol @atom:C 0.0 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom:C 100.0 + } + + write_once("In Settings") { + # If for some reason there are multiple chaperones present, + # I assume that they interact repulsively (hence, L=0) + # i j epsilon sigma K L + + pair_coeff @atom:C @atom:C lj/charmm/coul/charmm/inter 1.0 6.0 1 0 + + # Optional: define the atoms in the "chaperonins" group: + # (Defining a group for the chaperone makes it easy to immobilize it later.) + + group chaperonins type @atom:C + } + + + # Specify which pair_styles, and atom styles work well with + # this model. (Again this can be overridden later.) + + write_once("In Init") { + units lj + atom_style full + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 11.0 12.0 + } + +} # Chaperonin + +# We have not specified how this particle interacts with other particles +# besides itself. Later on you must do this. diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py new file mode 100755 index 0000000000..9b86809cc3 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py @@ -0,0 +1,87 @@ +#!/usr/bin/env python + +# Calculate a table of pairwise energies and forces between atoms in the +# protein and a chaperone provided in the supplemental materials section of: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# This is stored in a tabulated force field with a singularity at a distance R. +# +# To calculate the table for interaction between +# ...the chaperone and a hydrophobic bead (2004 PNAS paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 6.0 0.475 0.0 5.9 1181 +# ...the chaperone and a hydrophilic bead (2004 PNAS paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 6.0 0.0 0.0 5.9 1181 +# ...the chaperone and a hydrophobic bead (2006 JMB paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 3.0 0.60 3.1 8.0 981 True +# ...the chaperone and a hydrophilic bead (2006 JMB paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 3.0 0.0 3.1 8.0 981 True + +from math import * +import sys + +def U(r, eps, sigma, R, h): + #print('r='+str(r)+' eps='+str(eps)+' s='+str(sigma)+' R='+str(R)+' h='+str(h)) + # Formula is undefined at r=0, but you can take the limit: + if r <= 0: + return 4.0*pi*R*R*4.0*eps*(pow((sigma/R), 12.0) + - h*pow((sigma/R), 6.0)) + xp = sigma/(r+R) + xm = sigma/(r-R) + term10 = pow(xm, 10.0) - pow(xp, 10.0) + term4 = pow(xm, 4.0) - pow(xp, 4.0) + return 4.0*pi*eps*(R/r) * (0.2*term10 - 0.5*h*term4) + +def F(r, eps, sigma, R, h): + # Formula is undefined at r=0, but you can take the limit: + if r <= 0: + return 0.0 + product_term_a = U(r, eps, sigma, R, h) / r + ixp = (r+R)/sigma + ixm = (r-R)/sigma + dix_dr = 1.0/sigma + term10 = (10.0/sigma)*(pow(ixm, -11.0) - pow(ixp, -11.0)) + term4 = (4.0/sigma)*(pow(ixm, -5.0) - pow(ixp, -5.0)) + product_term_b = 4.0*eps*pi*(R/r) * (0.2*term10 - 0.5*h*term4) + return product_term_a + product_term_b + + +class InputError(Exception): + """ A generic exception object containing a string for error reporting. + + """ + def __init__(self, err_msg): + self.err_msg = err_msg + def __str__(self): + return self.err_msg + def __repr__(self): + return str(self) + +if len(sys.argv) < 8: + sys.stderr.write("Error: expected 7 arguments:\n" + "\n" + "Usage: "+sys.argv[0]+" epsilon sigma R h rmin rmax N\n\n") + sys.exit(-1) + +epsilon = float(sys.argv[1]) +sigma = float(sys.argv[2]) +R = float(sys.argv[3]) +h = float(sys.argv[4]) +rmin = float(sys.argv[5]) +rmax = float(sys.argv[6]) +N = int(sys.argv[7]) + +subtract_Urcut = False +if len(sys.argv) == 9: + subtract_Urcut = True +rcut = rmax + +for i in range(0,N): + r = rmin + i*(rmax-rmin)/(N-1) + U_r = U(r, epsilon, sigma, R, h) + F_r = F(r, epsilon, sigma, R, h) + if subtract_Urcut: + U_r -= U(rcut, epsilon, sigma, R, h) + if (r >= rcut) or (i==N-1): + U_r = 0.0 + F_r = 0.0 + print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_dihedral_table.py b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_dihedral_table.py new file mode 100755 index 0000000000..34c66418a8 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_dihedral_table.py @@ -0,0 +1,67 @@ +#!/usr/bin/env python + +# Calculate a table of dihedral angle interactions used in the alpha-helix +# and beta-sheet regions of the frustrated protein model described in +# provided in figure 8 of the supplemental materials section of: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# Note that the "A" and "B" parameters were incorrectly reported to be +# 5.4*epsilon and 6.0*epsilon. The values used were 5.6 and 6.0 epsilon. +# The phiA and phiB values were 57.29577951308232 degrees (1 rad) +# and 180 degrees, respectively. Both expA and expB were 6.0. +# +# To generate the table used for the alpha-helix (1 degree resolution) use this: +# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 +# To generate the table used for the beta-sheets (1 degree resolution) use this: +# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360 +# +# (If you're curious as to why I set the location of the minima at phi_alpha +# to 1.0 radians (57.2957795 degrees), there was no particularly good reason. +# I think the correct value turns out to be something closer to 50 degrees.) + + +from math import * +import sys + + +# The previous version included the repulsive core term +def U(phi, A, phiA, expA, B, phiB, expB, use_radians=False): + conv_units = pi/180.0 + if use_radians: + conv_units = 1.0 + termA = pow(cos(0.5*(phi-phiA)*conv_units), expA) + termB = pow(cos(0.5*(phi-phiB)*conv_units), expB) + return -A*termA - B*termB + +# The previous version included the repulsive core term +def F(phi, A, phiA, expA, B, phiB, expB, use_radians=False): + conv_units = pi/180.0 + if use_radians: + conv_units = 1.0 + termA = (0.5*sin(0.5*(phi-phiA)*conv_units) * + expA * pow(cos(0.5*(phi-phiA)*conv_units), expA-1.0)) + termB = (0.5*sin(0.5*(phi-phiB)*conv_units) * + expB * pow(cos(0.5*(phi-phiB)*conv_units), expB-1.0)) + return -conv_units*(A*termA + B*termB) + +if len(sys.argv) != 10: + sys.stderr.write("Error: expected 9 arguments:\n" + "\n" + "Usage: "+sys.argv[0]+" A phiA expA B phiB expB phiMin phiMax N\n\n") + sys.exit(-1) + +A = float(sys.argv[1]) +phiA = float(sys.argv[2]) +expA = float(sys.argv[3]) +B = float(sys.argv[4]) +phiB = float(sys.argv[5]) +expB = float(sys.argv[6]) +phi_min = float(sys.argv[7]) +phi_max = float(sys.argv[8]) +N = int(sys.argv[9]) + +for i in range(0,N): + phi = phi_min + i*(phi_max - phi_min)/(N-1) + U_phi = U(phi, A, phiA, expA, B, phiB, expB, use_radians=False) + F_phi = F(phi, A, phiA, expA, B, phiB, expB, use_radians=False) + print(str(i+1)+' '+str(phi)+' '+str(U_phi)+' '+str(F_phi)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/system.lt new file mode 100644 index 0000000000..d70ea9b1f2 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/system.lt @@ -0,0 +1,45 @@ +write_once("Data Boundary") { + 0.0 20.0 xlo xhi + 0.0 20.0 ylo yhi + 0.0 20.0 zlo zhi +} + + +import "1beadFrustrated_variants.lt" +import "chaperonin.lt" + + +protein = new 1beadMisfolded # (frustrated protein, misfolded conformation) +chaperinin = new Chaperonin # (hollow chaperonin cavity. usually immobile) + + + +# ---- Now define interactions between the atoms in the protein ---- +# ---- (named "B", "L", "N") and the atom which represents the ---- +# ---- chaperone ("C"). These interactions are tabulated. ---- + +write_once("In Settings") { + pair_coeff @atom:Chaperonin/C @atom:1beadFrustrated/B table table_chaperonin_h=0.475.dat CH_H0.475 + pair_coeff @atom:Chaperonin/C @atom:1beadFrustrated/L table table_chaperonin_h=0.dat CH_H0 + pair_coeff @atom:Chaperonin/C @atom:1beadFrustrated/N table table_chaperonin_h=0.dat CH_H0 +} + +# Note: If you want to use a "hydrophilic" chaperone (with h=0, not h=0.475) +# then replace "table_chaperonin_h=0_475.dat CH_H0.475" +# with "table_chaperonin_h=0.dat CH_H0" + +# LAMMPS has many available force field styles (and atom styles). Here we +# select the ones which work well for the full combine system. (This should +# override any settings made in "1beadFrustrated.lt" or "chaperonin.lt") + + +write_once("In Init") { + units lj + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid table spline 360 + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 table spline 1181 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) +} diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat new file mode 100644 index 0000000000..675d228a90 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat @@ -0,0 +1,1188 @@ +# Interaction between a chaperonin wall and hydrophobic ("B") beads (h=0.475). +# LAMMPS would crash unless I set the minimum radius to a positive value (not 0) + +CH_H0.475 +N 1181 R 0.00000000001 5.9 + +1 0.00000000001 -0.018422088583 0.0 +2 0.005 -0.0184221525389 2.55824082873e-05 +3 0.01 -0.0184223444081 5.11654127471e-05 +4 0.015 -0.018422664195 7.67496107175e-05 +5 0.02 -0.0184231119071 0.000102335598797 +6 0.025 -0.018423687555 0.000127923973785 +7 0.03 -0.0184243911519 0.000153515332637 +8 0.035 -0.0184252227143 0.000179110272379 +9 0.04 -0.0184261822615 0.000204709390236 +10 0.045 -0.0184272698161 0.000230313283607 +11 0.05 -0.0184284854033 0.000255922550119 +12 0.055 -0.0184298290516 0.000281537787625 +13 0.06 -0.0184313007922 0.000307159594253 +14 0.065 -0.0184329006595 0.000332788568419 +15 0.07 -0.0184346286908 0.000358425308862 +16 0.075 -0.0184364849265 0.000384070414671 +17 0.08 -0.0184384694099 0.000409724485298 +18 0.085 -0.0184405821873 0.000435388120601 +19 0.09 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5.855 626872755.056 -43125823862.6 +1173 5.86 889629660.718 -63393502739.0 +1174 5.865 1278740106.83 -94503868935.1 +1175 5.87 1863446791.23 -1.43025101229e+11 +1176 5.875 2756012237.96 -2.20012469835e+11 +1177 5.88 4141901662.1 -3.44454801129e+11 +1178 5.885 6333810219.82 -5.49690750348e+11 +1179 5.89 9870702215.02 -8.95661856872e+11 +1180 5.895 15704120493.1 -1.49296797827e+12 +1181 5.9 25558689542.6 -2.55153879404e+12 + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat new file mode 100644 index 0000000000..2ad6d7b691 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat @@ -0,0 +1,1187 @@ +# Interaction between a chaperonin wall and hydrophilic beads (type L or N, h=0) + +CH_H0 +N 1181 R 0.00000000001 5.9 + +1 0.00000000001 8.31299178857e-07 0.0 +2 0.005 8.31311879342e-07 -5.08022586688e-09 +3 0.01 8.31349981758e-07 -1.01608369733e-08 +4 0.015 8.31413488996e-07 -1.52422186449e-08 +5 0.02 8.31502405871e-07 -2.03247562721e-08 +6 0.025 8.31616739127e-07 -2.54088353865e-08 +7 0.03 8.31756497437e-07 -3.04948417048e-08 +8 0.035 8.319216914e-07 -3.55831611709e-08 +9 0.04 8.32112333547e-07 -4.06741800058e-08 +10 0.045 8.32328438343e-07 -4.57682847516e-08 +11 0.05 8.32570022183e-07 -5.08658623183e-08 +12 0.055 8.328371034e-07 -5.59673000292e-08 +13 0.06 8.33129702263e-07 -6.10729856679e-08 +14 0.065 8.33447840983e-07 -6.61833075238e-08 +15 0.07 8.33791543713e-07 -7.12986544391e-08 +16 0.075 8.34160836552e-07 -7.64194158551e-08 +17 0.08 8.34555747546e-07 -8.15459818584e-08 +18 0.085 8.34976306696e-07 -8.66787432278e-08 +19 0.09 8.35422545957e-07 -9.18180914814e-08 +20 0.095 8.35894499243e-07 -9.69644189231e-08 +21 0.1 8.36392202433e-07 -1.0211811869e-07 +22 0.105 8.36915693374e-07 -1.07279584798e-07 +23 0.11 8.37465011883e-07 -1.12449212192e-07 +24 0.115 8.38040199757e-07 -1.17627396792e-07 +25 0.12 8.38641300774e-07 -1.22814535539e-07 +26 0.125 8.392683607e-07 -1.28011026445e-07 +27 0.13 8.39921427291e-07 -1.33217268641e-07 +28 0.135 8.40600550305e-07 -1.38433662423e-07 +29 0.14 8.41305781504e-07 -1.43660609303e-07 +30 0.145 8.42037174658e-07 -1.48898512057e-07 +31 0.15 8.42794785557e-07 -1.54147774771e-07 +32 0.155 8.43578672015e-07 -1.59408802894e-07 +33 0.16 8.44388893873e-07 -1.64682003285e-07 +34 0.165 8.45225513015e-07 -1.69967784262e-07 +35 0.17 8.46088593367e-07 -1.75266555654e-07 +36 0.175 8.46978200908e-07 -1.80578728847e-07 +37 0.18 8.4789440368e-07 -1.85904716839e-07 +38 0.185 8.48837271792e-07 -1.91244934288e-07 +39 0.19 8.49806877432e-07 -1.96599797561e-07 +40 0.195 8.50803294874e-07 -2.01969724788e-07 +41 0.2 8.51826600486e-07 -2.07355135913e-07 +42 0.205 8.52876872743e-07 -2.12756452745e-07 +43 0.21 8.5395419223e-07 -2.18174099007e-07 +44 0.215 8.55058641658e-07 -2.23608500394e-07 +45 0.22 8.56190305871e-07 -2.29060084623e-07 +46 0.225 8.57349271858e-07 -2.34529281482e-07 +47 0.23 8.5853562876e-07 -2.40016522891e-07 +48 0.235 8.59749467885e-07 -2.4552224295e-07 +49 0.24 8.60990882715e-07 -2.51046877993e-07 +50 0.245 8.62259968921e-07 -2.56590866647e-07 +51 0.25 8.63556824372e-07 -2.62154649881e-07 +52 0.255 8.64881549149e-07 -2.67738671065e-07 +53 0.26 8.66234245555e-07 -2.73343376025e-07 +54 0.265 8.67615018129e-07 -2.78969213098e-07 +55 0.27 8.69023973658e-07 -2.84616633187e-07 +56 0.275 8.70461221189e-07 -2.90286089823e-07 +57 0.28 8.71926872044e-07 -2.95978039217e-07 +58 0.285 8.73421039834e-07 -3.0169294032e-07 +59 0.29 8.74943840469e-07 -3.07431254881e-07 +60 0.295 8.76495392179e-07 -3.13193447505e-07 +61 0.3 8.7807581552e-07 -3.18979985713e-07 +62 0.305 8.79685233396e-07 -3.24791340003e-07 +63 0.31 8.8132377107e-07 -3.30627983906e-07 +64 0.315 8.82991556179e-07 -3.36490394052e-07 +65 0.32 8.84688718753e-07 -3.42379050225e-07 +66 0.325 8.86415391229e-07 -3.48294435432e-07 +67 0.33 8.88171708466e-07 -3.54237035959e-07 +68 0.335 8.89957807764e-07 -3.60207341438e-07 +69 0.34 8.91773828877e-07 -3.66205844906e-07 +70 0.345 8.93619914037e-07 -3.72233042875e-07 +71 0.35 8.95496207963e-07 -3.78289435392e-07 +72 0.355 8.97402857887e-07 -3.84375526106e-07 +73 0.36 8.99340013567e-07 -3.90491822333e-07 +74 0.365 9.01307827305e-07 -3.96638835124e-07 +75 0.37 9.0330645397e-07 -4.02817079329e-07 +76 0.375 9.05336051015e-07 -4.09027073668e-07 +77 0.38 9.07396778494e-07 -4.152693408e-07 +78 0.385 9.09488799088e-07 -4.21544407387e-07 +79 0.39 9.11612278118e-07 -4.2785280417e-07 +80 0.395 9.13767383571e-07 -4.34195066035e-07 +81 0.4 9.15954286119e-07 -4.40571732086e-07 +82 0.405 9.18173159138e-07 -4.46983345718e-07 +83 0.41 9.20424178735e-07 -4.53430454687e-07 +84 0.415 9.22707523764e-07 -4.59913611186e-07 +85 0.42 9.25023375853e-07 -4.66433371919e-07 +86 0.425 9.27371919425e-07 -4.72990298174e-07 +87 0.43 9.29753341721e-07 -4.795849559e-07 +88 0.435 9.32167832821e-07 -4.86217915785e-07 +89 0.44 9.34615585674e-07 -4.9288975333e-07 +90 0.445 9.37096796117e-07 -4.99601048932e-07 +91 0.45 9.39611662902e-07 -5.0635238796e-07 +92 0.455 9.4216038772e-07 -5.13144360835e-07 +93 0.46 9.44743175226e-07 -5.19977563112e-07 +94 0.465 9.47360233068e-07 -5.26852595561e-07 +95 0.47 9.50011771908e-07 -5.33770064252e-07 +96 0.475 9.52698005456e-07 -5.40730580635e-07 +97 0.48 9.55419150489e-07 -5.47734761627e-07 +98 0.485 9.58175426884e-07 -5.54783229699e-07 +99 0.49 9.60967057644e-07 -5.61876612959e-07 +100 0.495 9.63794268928e-07 -5.69015545241e-07 +101 0.5 9.66657290077e-07 -5.76200666196e-07 +102 0.505 9.69556353647e-07 -5.83432621378e-07 +103 0.51 9.72491695434e-07 -5.90712062337e-07 +104 0.515 9.75463554509e-07 -5.9803964671e-07 +105 0.52 9.78472173246e-07 -6.05416038315e-07 +106 0.525 9.81517797354e-07 -6.12841907243e-07 +107 0.53 9.84600675908e-07 -6.20317929954e-07 +108 0.535 9.87721061381e-07 -6.27844789373e-07 +109 0.54 9.90879209678e-07 -6.3542317499e-07 +110 0.545 9.94075380168e-07 -6.43053782955e-07 +111 0.55 9.97309835716e-07 -6.50737316177e-07 +112 0.555 1.00058284272e-06 -6.58474484431e-07 +113 0.56 1.00389467115e-06 -6.66266004455e-07 +114 0.565 1.00724559456e-06 -6.74112600053e-07 +115 0.57 1.01063589016e-06 -6.82015002204e-07 +116 0.575 1.01406583882e-06 -6.89973949166e-07 +117 0.58 1.01753572513e-06 -6.97990186581e-07 +118 0.585 1.02104583743e-06 -7.06064467589e-07 +119 0.59 1.02459646782e-06 -7.14197552934e-07 +120 0.595 1.02818791224e-06 -7.22390211075e-07 +121 0.6 1.03182047051e-06 -7.30643218304e-07 +122 0.605 1.03549444631e-06 -7.38957358854e-07 +123 0.61 1.0392101473e-06 -7.47333425021e-07 +124 0.615 1.04296788511e-06 -7.55772217275e-07 +125 0.62 1.04676797537e-06 -7.64274544386e-07 +126 0.625 1.0506107378e-06 -7.72841223537e-07 +127 0.63 1.05449649623e-06 -7.81473080451e-07 +128 0.635 1.05842557863e-06 -7.90170949513e-07 +129 0.64 1.06239831715e-06 -7.98935673896e-07 +130 0.645 1.06641504821e-06 -8.07768105686e-07 +131 0.65 1.07047611249e-06 -8.1666910601e-07 +132 0.655 1.074581855e-06 -8.25639545171e-07 +133 0.66 1.07873262514e-06 -8.34680302772e-07 +134 0.665 1.08292877671e-06 -8.43792267857e-07 +135 0.67 1.08717066799e-06 -8.52976339042e-07 +136 0.675 1.09145866179e-06 -8.62233424653e-07 +137 0.68 1.09579312546e-06 -8.71564442867e-07 +138 0.685 1.10017443099e-06 -8.80970321849e-07 +139 0.69 1.10460295501e-06 -8.90451999898e-07 +140 0.695 1.1090790789e-06 -9.0001042559e-07 +141 0.7 1.11360318878e-06 -9.09646557926e-07 +142 0.705 1.1181756756e-06 -9.19361366479e-07 +143 0.71 1.1227969352e-06 -9.29155831544e-07 +144 0.715 1.12746736833e-06 -9.39030944294e-07 +145 0.72 1.13218738073e-06 -9.48987706931e-07 +146 0.725 1.13695738317e-06 -9.59027132844e-07 +147 0.73 1.14177779154e-06 -9.6915024677e-07 +148 0.735 1.14664902685e-06 -9.79358084952e-07 +149 0.74 1.15157151534e-06 -9.89651695304e-07 +150 0.745 1.15654568852e-06 -1.00003213758e-06 +151 0.75 1.16157198322e-06 -1.01050048352e-06 +152 0.755 1.16665084166e-06 -1.02105781707e-06 +153 0.76 1.17178271153e-06 -1.0317052345e-06 +154 0.765 1.176968046e-06 -1.0424438446e-06 +155 0.77 1.18220730383e-06 -1.05327476888e-06 +156 0.775 1.18750094943e-06 -1.0641991417e-06 +157 0.78 1.19284945291e-06 -1.07521811051e-06 +158 0.785 1.19825329013e-06 -1.08633283599e-06 +159 0.79 1.20371294282e-06 -1.09754449225e-06 +160 0.795 1.20922889858e-06 -1.10885426703e-06 +161 0.8 1.21480165102e-06 -1.12026336191e-06 +162 0.805 1.22043169976e-06 -1.13177299243e-06 +163 0.81 1.22611955055e-06 -1.14338438839e-06 +164 0.815 1.23186571533e-06 -1.15509879397e-06 +165 0.82 1.23767071227e-06 -1.16691746799e-06 +166 0.825 1.24353506591e-06 -1.17884168407e-06 +167 0.83 1.24945930716e-06 -1.19087273088e-06 +168 0.835 1.25544397344e-06 -1.20301191233e-06 +169 0.84 1.26148960871e-06 -1.21526054778e-06 +170 0.845 1.26759676357e-06 -1.22761997229e-06 +171 0.85 1.27376599533e-06 -1.2400915368e-06 +172 0.855 1.27999786811e-06 -1.2526766084e-06 +173 0.86 1.2862929529e-06 -1.26537657052e-06 +174 0.865 1.29265182763e-06 -1.27819282318e-06 +175 0.87 1.29907507731e-06 -1.29112678323e-06 +176 0.875 1.30556329404e-06 -1.30417988457e-06 +177 0.88 1.31211707714e-06 -1.31735357842e-06 +178 0.885 1.31873703325e-06 -1.33064933354e-06 +179 0.89 1.32542377639e-06 -1.34406863648e-06 +180 0.895 1.33217792804e-06 -1.35761299185e-06 +181 0.9 1.33900011726e-06 -1.37128392257e-06 +182 0.905 1.34589098079e-06 -1.38508297012e-06 +183 0.91 1.35285116309e-06 -1.39901169482e-06 +184 0.915 1.3598813165e-06 -1.41307167609e-06 +185 0.92 1.36698210128e-06 -1.42726451271e-06 +186 0.925 1.37415418575e-06 -1.44159182311e-06 +187 0.93 1.38139824636e-06 -1.45605524565e-06 +188 0.935 1.38871496782e-06 -1.47065643891e-06 +189 0.94 1.39610504317e-06 -1.48539708196e-06 +190 0.945 1.40356917389e-06 -1.50027887466e-06 +191 0.95 1.41110807003e-06 -1.51530353796e-06 +192 0.955 1.41872245029e-06 -1.5304728142e-06 +193 0.96 1.42641304213e-06 -1.54578846742e-06 +194 0.965 1.4341805819e-06 -1.56125228366e-06 +195 0.97 1.44202581492e-06 -1.57686607128e-06 +196 0.975 1.44994949562e-06 -1.59263166129e-06 +197 0.98 1.45795238763e-06 -1.60855090765e-06 +198 0.985 1.46603526391e-06 -1.62462568762e-06 +199 0.99 1.47419890689e-06 -1.64085790209e-06 +200 0.995 1.48244410853e-06 -1.65724947591e-06 +201 1.0 1.4907716705e-06 -1.67380235825e-06 +202 1.005 1.49918240425e-06 -1.69051852294e-06 +203 1.01 1.50767713119e-06 -1.70739996882e-06 +204 1.015 1.51625668278e-06 -1.72444872011e-06 +205 1.02 1.52492190065e-06 -1.74166682675e-06 +206 1.025 1.53367363676e-06 -1.75905636483e-06 +207 1.03 1.54251275352e-06 -1.77661943691e-06 +208 1.035 1.5514401239e-06 -1.7943581724e-06 +209 1.04 1.56045663161e-06 -1.81227472801e-06 +210 1.045 1.56956317119e-06 -1.83037128807e-06 +211 1.05 1.57876064818e-06 -1.84865006497e-06 +212 1.055 1.58804997927e-06 -1.86711329958e-06 +213 1.06 1.59743209239e-06 -1.88576326162e-06 +214 1.065 1.60690792693e-06 -1.90460225011e-06 +215 1.07 1.61647843382e-06 -1.92363259378e-06 +216 1.075 1.62614457572e-06 -1.94285665153e-06 +217 1.08 1.63590732717e-06 -1.9622768128e-06 +218 1.085 1.64576767472e-06 -1.98189549811e-06 +219 1.09 1.65572661711e-06 -2.00171515944e-06 +220 1.095 1.66578516541e-06 -2.02173828072e-06 +221 1.1 1.67594434321e-06 -2.04196737828e-06 +222 1.105 1.68620518674e-06 -2.06240500133e-06 +223 1.11 1.69656874507e-06 -2.08305373245e-06 +224 1.115 1.70703608027e-06 -2.10391618807e-06 +225 1.12 1.71760826757e-06 -2.12499501897e-06 +226 1.125 1.72828639555e-06 -2.14629291076e-06 +227 1.13 1.73907156631e-06 -2.16781258443e-06 +228 1.135 1.74996489563e-06 -2.18955679685e-06 +229 1.14 1.76096751317e-06 -2.21152834128e-06 +230 1.145 1.77208056264e-06 -2.23373004793e-06 +231 1.15 1.78330520203e-06 -2.2561647845e-06 +232 1.155 1.79464260371e-06 -2.27883545672e-06 +233 1.16 1.80609395472e-06 -2.30174500894e-06 +234 1.165 1.8176604569e-06 -2.32489642465e-06 +235 1.17 1.82934332711e-06 -2.34829272711e-06 +236 1.175 1.84114379742e-06 -2.3719369799e-06 +237 1.18 1.85306311533e-06 -2.39583228755e-06 +238 1.185 1.86510254397e-06 -2.41998179612e-06 +239 1.19 1.87726336227e-06 -2.44438869382e-06 +240 1.195 1.88954686527e-06 -2.46905621166e-06 +241 1.2 1.90195436421e-06 -2.49398762405e-06 +242 1.205 1.91448718686e-06 -2.51918624948e-06 +243 1.21 1.92714667767e-06 -2.54465545114e-06 +244 1.215 1.93993419801e-06 -2.57039863763e-06 +245 1.22 1.95285112644e-06 -2.59641926361e-06 +246 1.225 1.96589885888e-06 -2.62272083047e-06 +247 1.23 1.97907880889e-06 -2.64930688708e-06 +248 1.235 1.99239240789e-06 -2.67618103045e-06 +249 1.24 2.00584110541e-06 -2.7033469065e-06 +250 1.245 2.01942636933e-06 -2.73080821073e-06 +251 1.25 2.03314968614e-06 -2.75856868904e-06 +252 1.255 2.04701256117e-06 -2.78663213843e-06 +253 1.26 2.06101651889e-06 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0000000000..d660fee308 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_dihedral_frustrated.dat @@ -0,0 +1,735 @@ +# Table of the potential and its negative derivative for frustrated alpha helix +# (Note: Derivatives are in units of energy/radians, not energy/degrees.) +# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 + +FRUSTRATED_ALPHA +N 360 DEGREES + +1 0.0 -2.74081145103 0.0783990792662 +2 1.0 -2.81950869101 0.0789852583442 +3 2.0 -2.89876136749 0.0795096391909 +4 3.0 -2.97850675562 0.0799703813963 +5 4.0 -3.05868032959 0.0803657243943 +6 5.0 -3.13921584545 0.0806939935737 +7 6.0 -3.22004543014 0.0809536062381 +8 7.0 -3.30109967628 0.0811430773977 +9 8.0 -3.38230774267 0.0812610253741 +10 9.0 -3.46359746038 0.0813061772009 +11 10.0 -3.54489544401 0.0812773738039 +12 11.0 -3.62612720812 0.0811735749433 +13 12.0 -3.70721728841 0.0809938639029 +14 13.0 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-1.53878331313 0.061018148454 +345 344.0 -1.60045794659 0.0623272072653 +346 345.0 -1.66342954101 0.0636117049668 +347 346.0 -1.72767243359 0.0648694329207 +348 347.0 -1.79315873807 0.0660981537565 +349 348.0 -1.85985831882 0.0672956071568 +350 349.0 -1.92773877092 0.0684595158069 +351 350.0 -1.99676540616 0.0695875914917 +352 351.0 -2.06690124527 0.0706775413231 +353 352.0 -2.13810701636 0.0717270740805 +354 353.0 -2.21034115987 0.0727339066469 +355 354.0 -2.28355983986 0.0736957705223 +356 355.0 -2.35771696194 0.0746104183955 +357 356.0 -2.43276419776 0.0754756307561 +358 357.0 -2.50865101613 0.0762892225281 +359 358.0 -2.58532472075 0.0770490497051 +360 359.0 -2.66273049463 0.0777530159679 + +# Table of the potential and its negative derivative for frustrated beta sheet +# (Note: Derivatives are in units of energy/radians, not energy/degrees.) +# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360 + +FRUSTRATED_BETA +N 360 DEGREES + +1 0.0 -2.55809068762 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0.0704439199439 +358 357.0 -2.3414076153 0.0712032738621 +359 358.0 -2.41296973939 0.0719124463259 +360 359.0 -2.48521512832 0.072569481568 diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.min b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.min new file mode 100644 index 0000000000..321ba3c095 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.min @@ -0,0 +1,25 @@ +# -- Init section -- + +include system.in.init + +# -- Atom definition section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# Optional: Make sure the pairwise energies look reasonable: +pair_write 1 4 1001 r 0.00000000001 5.05 test_chap-B.dat C-B 0 0 +pair_write 2 4 1001 r 0.00000000001 5.05 test_chap-L.dat C-L 0 0 +pair_write 3 4 1001 r 0.00000000001 5.05 test_chap-N.dat C-N 0 0 + + +# -- Run section -- + +dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz + +minimize 1.0e-5 1.0e-7 500 2000 + +write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.nvt new file mode 100644 index 0000000000..7c0855cb8d --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.nvt @@ -0,0 +1,48 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +# I you want to be careful, you can minimize the system first. (Try using +# "run.in.min" and uncomment the read_restart command in this file below.) +# read_restart system_after_min.rst + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 0.025 +dump 1 all custom 50000 traj_nvt.lammpstrj id mol type x y z ix iy iz + +# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". +# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) + +# Keep the chaperonin fixed. Only let the protein move. + +fix fxlan proteins langevin 0.25 0.25 1.0 48279 +fix fxnve proteins nve + +# Notes: +# The temperature is in reduced units and is set to 0.25 +# which is the folding temperature for the frustrated protein +# The inverse-damping-rate "damp" (which has units of time) is set to 1.0, +# as it was in the paper. (Hopefully folding times should be similar.) +# (See http://lammps.sandia.gov/doc/fix_langevin.html) + + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo_modify norm no #(report total energy not energy / num_atoms) +thermo 50000 #(time interval for printing out "thermo" data) + +#restart 100000000 restart_nvt + +run 1000000000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README.TXT new file mode 100644 index 0000000000..ecb9adad2e --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README.TXT @@ -0,0 +1,38 @@ +# This directory demonstrates how to run a long simulation of +# the "frustrated" coarse-grained protein in the presence of one +# or more coarse-graine small ("mini") chaperones (R=3, h=0.6) as described in: +# +# AI Jewett and J-E Shea, J. Mol. Biol, Vol 363(5), (2006) +# and earlier in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# +# Because this process takes a long time (even with the help of the chaperone) +# I save the data relatively infrequently. +# +# Note: In the 2006 paper, only one protein and one chaperone was simulated. +# In this example, 8 proteins and 8 chaperones were simulated. +# +# Note: In this case, the chaperones appear to catalyze aggregation. +# This is due to an artifact in the protein model. That model +# was not designed to study aggregation. However the simulation +# is suitable for making pretty pictures (to show off moltemplate). +# +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. + +------------- +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh new file mode 100755 index 0000000000..45bd2d451d --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh @@ -0,0 +1,31 @@ +# You would probably run lammps this way: +# +# lmp_ubuntu -i run.in.nvt + +# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer +# to the input scripts & data files you created earlier when you ran moltemplate +# system.in.init, system.in.settings, system.data + + + + +# ----------------------------------- + + + +LAMMPS_COMMAND="lmp_ubuntu" + +# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps +# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. + +# Run lammps using the following 3 commands: + +"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +"$LAMMPS_COMMAND" -i run.in.nvt # production run + +# Alternately, if you have MPI installed, try something like this: + +#NUMPROCS=4 +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_setup.sh new file mode 100755 index 0000000000..f2462426f1 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_setup.sh @@ -0,0 +1,24 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -overlay-dihdedrals system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + cp -r table*.dat ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 0000000000..b0013ccc62 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,476 @@ +PSF + + 1 !NTITLE + REMARKS VMD generated structure x-plor psf file + + 224 !NATOM + 1 1 2 2 0.000000 1.0000 0 + 2 1 1 1 0.000000 1.0000 0 + 3 1 2 2 0.000000 1.0000 0 + 4 1 1 1 0.000000 1.0000 0 + 5 1 2 2 0.000000 1.0000 0 + 6 1 1 1 0.000000 1.0000 0 + 7 1 3 3 0.000000 1.0000 0 + 8 1 3 3 0.000000 1.0000 0 + 9 1 1 1 0.000000 1.0000 0 + 10 1 2 2 0.000000 1.0000 0 + 11 1 1 1 0.000000 1.0000 0 + 12 1 2 2 0.000000 1.0000 0 + 13 1 1 1 0.000000 1.0000 0 + 14 1 2 2 0.000000 1.0000 0 + 15 1 3 3 0.000000 1.0000 0 + 16 1 3 3 0.000000 1.0000 0 + 17 1 3 3 0.000000 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and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=67500tau_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated.lt new file mode 100644 index 0000000000..e43026ba9f --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated.lt @@ -0,0 +1,216 @@ +# This file defines the "frustrated" coarse-grained protein model used in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) + + +1beadFrustrated { + + # There are 3 atom types (referred to above as B, L, and N) + # Define their masses: + + write_once("Data Masses") { + @atom:B 1.0 + @atom:L 1.0 + @atom:N 1.0 + } + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol @atom:L 0.0 -0.92636654 -1.8409904 -2.1482679 + $atom:a2 $mol @atom:B 0.0 -0.57313354 -1.0670787 -1.6182341 + $atom:a3 $mol @atom:L 0.0 -0.85707399 -1.2358703 -0.69350966 + $atom:a4 $mol @atom:B 0.0 -0.44231274 -0.4584993 -0.23418709 + $atom:a5 $mol @atom:L 0.0 -0.75081182 -0.62868078 0.69786737 + $atom:a6 $mol @atom:B 0.0 -0.36201977 0.11619615 1.2249098 + $atom:a7 $mol @atom:N 0.0 -0.63708237 -0.15973084 2.1723919 + $atom:a8 $mol @atom:N 0.0 0.20516047 0.10417157 2.624901 + $atom:a9 $mol @atom:B 0.0 0.57223743 0.44728103 1.7695617 + $atom:a10 $mol @atom:L 0.0 0.77646279 -0.40630393 1.3168043 + $atom:a11 $mol @atom:B 0.0 0.45475664 -0.2077937 0.40045721 + $atom:a12 $mol @atom:L 0.0 0.72712495 -1.0397637 -0.087614951 + $atom:a13 $mol @atom:B 0.0 0.36971183 -0.85840501 -0.9933019 + $atom:a14 $mol @atom:L 0.0 0.74784336 -1.5700415 -1.5859217 + $atom:a15 $mol @atom:N 0.0 0.43423905 -1.2758917 -2.4853429 + $atom:a16 $mol @atom:N 0.0 0.70583191 -0.30726921 -2.4987711 + $atom:a17 $mol @atom:N 0.0 -0.091688915 0.23323014 -2.2051358 + $atom:a18 $mol @atom:B 0.0 -0.34243283 -0.035822049 -1.2644719 + $atom:a19 $mol @atom:B 0.0 0.41961247 0.18475451 -0.65971014 + $atom:a20 $mol @atom:L 0.0 0.51968465 1.1546791 -0.77877053 + $atom:a21 $mol @atom:L 0.0 -0.40827985 1.2765273 -0.52550748 + $atom:a22 $mol @atom:B 0.0 -0.368141 0.58090904 0.19152224 + $atom:a23 $mol @atom:B 0.0 0.40327249 0.86101769 0.7336255 + $atom:a24 $mol @atom:L 0.0 0.22707289 1.8326235 0.89673346 + $atom:a25 $mol @atom:L 0.0 -0.66500182 1.7285809 1.2783166 + $atom:a26 $mol @atom:B 0.0 -0.39205603 1.0475436 1.9328097 + $atom:a27 $mol @atom:L 0.0 0.25339027 1.5246265 2.5388463 + } + + # bond-ID bond-Type atom-ID atom-ID + + write('Data Bonds') { + $bond:b1 @bond:backbone $atom:a1 $atom:a2 + $bond:b2 @bond:backbone $atom:a2 $atom:a3 + $bond:b3 @bond:backbone $atom:a3 $atom:a4 + $bond:b4 @bond:backbone $atom:a4 $atom:a5 + $bond:b5 @bond:backbone $atom:a5 $atom:a6 + $bond:b6 @bond:backbone $atom:a6 $atom:a7 + $bond:b7 @bond:backbone $atom:a7 $atom:a8 + $bond:b8 @bond:backbone $atom:a8 $atom:a9 + $bond:b9 @bond:backbone $atom:a9 $atom:a10 + $bond:b10 @bond:backbone $atom:a10 $atom:a11 + $bond:b11 @bond:backbone $atom:a11 $atom:a12 + $bond:b12 @bond:backbone $atom:a12 $atom:a13 + $bond:b13 @bond:backbone $atom:a13 $atom:a14 + $bond:b14 @bond:backbone $atom:a14 $atom:a15 + $bond:b15 @bond:backbone $atom:a15 $atom:a16 + $bond:b16 @bond:backbone $atom:a16 $atom:a17 + $bond:b17 @bond:backbone $atom:a17 $atom:a18 + $bond:b18 @bond:backbone $atom:a18 $atom:a19 + $bond:b19 @bond:backbone $atom:a19 $atom:a20 + $bond:b20 @bond:backbone $atom:a20 $atom:a21 + $bond:b21 @bond:backbone $atom:a21 $atom:a22 + $bond:b22 @bond:backbone $atom:a22 $atom:a23 + $bond:b23 @bond:backbone $atom:a23 $atom:a24 + $bond:b24 @bond:backbone $atom:a24 $atom:a25 + $bond:b25 @bond:backbone $atom:a25 $atom:a26 + $bond:b26 @bond:backbone $atom:a26 $atom:a27 + } + + # (3-body) Angles are specified below + + # (4-body) Dihedrals must be defined explicitly for every quartet of atoms. + # (These interactions are not determined by atom type.) + + # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID + + write('Data Dihedrals') { + + $dihedral:d1 @dihedral:beta $atom:a1 $atom:a2 $atom:a3 $atom:a4 + $dihedral:d2 @dihedral:beta $atom:a2 $atom:a3 $atom:a4 $atom:a5 + $dihedral:d3 @dihedral:beta $atom:a3 $atom:a4 $atom:a5 $atom:a6 + $dihedral:d4 @dihedral:beta $atom:a4 $atom:a5 $atom:a6 $atom:a7 + + # Dihedral angle forces in the turn regions were switched off + # (in this model) so just I comment them out (and \ the variable names). + # \$dihedral:d5 \@dihedral:turn $atom:a5 $atom:a6 $atom:a7 $atom:a8 + # \$dihedral:d6 \@dihedral:turn $atom:a6 $atom:a7 $atom:a8 $atom:a9 + # \$dihedral:d7 \@dihedral:turn $atom:a7 $atom:a8 $atom:a9 $atom:a10 + + $dihedral:d8 @dihedral:beta $atom:a8 $atom:a9 $atom:a10 $atom:a11 + $dihedral:d9 @dihedral:beta $atom:a9 $atom:a10 $atom:a11 $atom:a12 + $dihedral:d10 @dihedral:beta $atom:a10 $atom:a11 $atom:a12 $atom:a13 + $dihedral:d11 @dihedral:beta $atom:a11 $atom:a12 $atom:a13 $atom:a14 + $dihedral:d12 @dihedral:beta $atom:a12 $atom:a13 $atom:a14 $atom:a15 + + # Dihedral angle forces in the turn regions were switched off + # (in this model) so just I comment them out (and \ the variable names). + # \$dihedral:d13 \@dihedral:turn $atom:a13 $atom:a14 $atom:a15 $atom:a16 + # \$dihedral:d14 \@dihedral:turn $atom:a14 $atom:a15 $atom:a16 $atom:a17 + + $dihedral:d15 @dihedral:alpha $atom:a15 $atom:a16 $atom:a17 $atom:a18 + $dihedral:d16 @dihedral:alpha $atom:a16 $atom:a17 $atom:a18 $atom:a19 + $dihedral:d17 @dihedral:alpha $atom:a17 $atom:a18 $atom:a19 $atom:a20 + $dihedral:d18 @dihedral:alpha $atom:a18 $atom:a19 $atom:a20 $atom:a21 + $dihedral:d19 @dihedral:alpha $atom:a19 $atom:a20 $atom:a21 $atom:a22 + $dihedral:d20 @dihedral:alpha $atom:a20 $atom:a21 $atom:a22 $atom:a23 + $dihedral:d21 @dihedral:alpha $atom:a21 $atom:a22 $atom:a23 $atom:a24 + $dihedral:d22 @dihedral:alpha $atom:a22 $atom:a23 $atom:a24 $atom:a25 + $dihedral:d23 @dihedral:alpha $atom:a23 $atom:a24 $atom:a25 $atom:a26 + $dihedral:d24 @dihedral:alpha $atom:a24 $atom:a25 $atom:a26 $atom:a27 + } + + # All consecutively bonded triplets of atoms same 3-body bond-angle + # interaction parameters. Of coarse, we could specify them all explicitly + # (as we did for the dihedrals above), but I wanted to show how to specify + # angles by atom type instead. (You can do this for dihedrals & impropers + # also.) + + # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type + + write_once('Data Angles By Type') { + @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* + } + + # (The "*" is a wildcard character. I use "*" to denote any atom-type or + # bond-type which is defined within the current namespace: 1beadFrustrated) + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 + pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0 + pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0 + pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1 + pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0 + pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0 + } + + + # 2-body (bonded) interactions: + # + # Ubond(r) = (k/2)*(r-0)^2 + # + # The corresponding command is: + # + # bond-Type bondstylename k r0 + + write_once("In Settings") { + bond_coeff @bond:backbone harmonic 100.0 1.0 + } + + # 3-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Uangle(theta) = (k/2)*(theta-theta0)^2 + # (k in kcal/mol/rad^2, theta0 in degrees) + # + # angle-Type anglestylename k theta0 + + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 13.3333333333 105.0 + } + + + # We use tabular dihedral potentials to implement the dihedral forces. + # (Actually there is a way to use Fourier series, using multiple charmm + # style dihedral interactions, but it's slower and messier.) + + write_once("In Settings") { + # style file keyword + dihedral_coeff @dihedral:alpha table table_dihedral_frustrated.dat FRUSTRATED_ALPHA + dihedral_coeff @dihedral:beta table table_dihedral_frustrated.dat FRUSTRATED_BETA + # No need to specify dihedral interactions in the turn regions. (none exist) + } + + write_once("In Settings") { + # Optional: define the atoms in the "proteins" group + group proteins type @atom:B + group proteins type @atom:L + group proteins type @atom:N + } + + # LAMMPS has many available force field styles (and atom styles). + # Here, we pick the ones which work well for this molecular model: + + write_once("In Init") { + # --- Default options for the "1BeadFrustrated" protein model --- + # --- (These can be overridden later.) --- + units lj + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid table spline 360 + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + +} # 1beadFrustrated + + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated_variants.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated_variants.lt new file mode 100644 index 0000000000..54e2de4376 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated_variants.lt @@ -0,0 +1,85 @@ +import "1beadFrustrated.lt" + + +# Alternate starting conformation (same molecule): + + +1beadMisfolded inherits 1beadFrustrated { + + # This molecule "inherits" all of its features from "1beadFrustrated". + # Here we override the atomic positions with new coordinates: + + # AtomID MoleculeID AtomType Charge X Y Z + + write("Data Atoms") { + $atom:a1 $mol @atom:L 0.0 -0.69801399 -0.22114168 -1.9464876 + $atom:a2 $mol @atom:B 0.0 -0.40921658 -0.027063664 -1.0033251 + $atom:a3 $mol @atom:L 0.0 0.10259348 0.80836418 -1.0737085 + $atom:a4 $mol @atom:B 0.0 0.25857916 1.0054984 -0.11621451 + $atom:a5 $mol @atom:L 0.0 0.8258629 1.8325549 -0.18529135 + $atom:a6 $mol @atom:B 0.0 0.91366257 2.1950317 0.74175977 + $atom:a7 $mol @atom:N 0.0 1.4399539 1.554238 1.2994409 + $atom:a8 $mol @atom:N 0.0 0.73372573 1.0161012 1.7397275 + $atom:a9 $mol @atom:B 0.0 0.26608782 0.65302497 0.94353938 + $atom:a10 $mol @atom:L 0.0 0.97442305 0.13574211 0.50586398 + $atom:a11 $mol @atom:B 0.0 0.35889617 -0.18247555 -0.1764186 + $atom:a12 $mol @atom:L 0.0 0.87151735 -0.77260824 -0.75240916 + $atom:a13 $mol @atom:B 0.0 0.047726486 -1.0530682 -1.1902704 + $atom:a14 $mol @atom:L 0.0 0.34530697 -1.7476773 -1.8393331 + $atom:a15 $mol @atom:N 0.0 0.65865186 -2.45948 -1.2167056 + $atom:a16 $mol @atom:N 0.0 -0.16534524 -2.6219442 -0.67112167 + $atom:a17 $mol @atom:N 0.0 -0.010590421 -2.2445242 0.24748633 + $atom:a18 $mol @atom:B 0.0 0.18135771 -1.2564919 0.1767523 + $atom:a19 $mol @atom:B 0.0 -0.57472665 -0.82852797 -0.27027791 + $atom:a20 $mol @atom:L 0.0 -1.3967448 -1.0516787 0.24247346 + $atom:a21 $mol @atom:L 0.0 -1.003428 -0.85642681 1.1107555 + $atom:a22 $mol @atom:B 0.0 -0.25156735 -0.3182346 0.74262946 + $atom:a23 $mol @atom:B 0.0 -0.61751956 0.30115562 0.070426493 + $atom:a24 $mol @atom:L 0.0 -1.3347934 0.83310182 0.52625934 + $atom:a25 $mol @atom:L 0.0 -0.83315257 1.270904 1.2564086 + $atom:a26 $mol @atom:B 0.0 -0.10469759 1.6988523 0.72597181 + $atom:a27 $mol @atom:L 0.0 -0.57854905 2.3367737 0.11206868 + } + +} # 1beadMisfolded + + +1beadUnfolded inherits 1beadFrustrated { + + # This molecule "inherits" all of its features from "1beadFrustrated" + # Here we override the atomic positions with new coordinates: + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0 + $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8 + $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8 + $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0 + $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0 + $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8 + $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8 + $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0 + $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0 + $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8 + $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8 + $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0 + $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0 + $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8 + $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8 + $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2 + $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2 + $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6 + $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6 + $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2 + $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2 + $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6 + $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6 + $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2 + $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2 + $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6 + $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6 + } + +} # 1beadUnfolded + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_chaperone_table.py b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_chaperone_table.py new file mode 100755 index 0000000000..9b86809cc3 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_chaperone_table.py @@ -0,0 +1,87 @@ +#!/usr/bin/env python + +# Calculate a table of pairwise energies and forces between atoms in the +# protein and a chaperone provided in the supplemental materials section of: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# This is stored in a tabulated force field with a singularity at a distance R. +# +# To calculate the table for interaction between +# ...the chaperone and a hydrophobic bead (2004 PNAS paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 6.0 0.475 0.0 5.9 1181 +# ...the chaperone and a hydrophilic bead (2004 PNAS paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 6.0 0.0 0.0 5.9 1181 +# ...the chaperone and a hydrophobic bead (2006 JMB paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 3.0 0.60 3.1 8.0 981 True +# ...the chaperone and a hydrophilic bead (2006 JMB paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 3.0 0.0 3.1 8.0 981 True + +from math import * +import sys + +def U(r, eps, sigma, R, h): + #print('r='+str(r)+' eps='+str(eps)+' s='+str(sigma)+' R='+str(R)+' h='+str(h)) + # Formula is undefined at r=0, but you can take the limit: + if r <= 0: + return 4.0*pi*R*R*4.0*eps*(pow((sigma/R), 12.0) + - h*pow((sigma/R), 6.0)) + xp = sigma/(r+R) + xm = sigma/(r-R) + term10 = pow(xm, 10.0) - pow(xp, 10.0) + term4 = pow(xm, 4.0) - pow(xp, 4.0) + return 4.0*pi*eps*(R/r) * (0.2*term10 - 0.5*h*term4) + +def F(r, eps, sigma, R, h): + # Formula is undefined at r=0, but you can take the limit: + if r <= 0: + return 0.0 + product_term_a = U(r, eps, sigma, R, h) / r + ixp = (r+R)/sigma + ixm = (r-R)/sigma + dix_dr = 1.0/sigma + term10 = (10.0/sigma)*(pow(ixm, -11.0) - pow(ixp, -11.0)) + term4 = (4.0/sigma)*(pow(ixm, -5.0) - pow(ixp, -5.0)) + product_term_b = 4.0*eps*pi*(R/r) * (0.2*term10 - 0.5*h*term4) + return product_term_a + product_term_b + + +class InputError(Exception): + """ A generic exception object containing a string for error reporting. + + """ + def __init__(self, err_msg): + self.err_msg = err_msg + def __str__(self): + return self.err_msg + def __repr__(self): + return str(self) + +if len(sys.argv) < 8: + sys.stderr.write("Error: expected 7 arguments:\n" + "\n" + "Usage: "+sys.argv[0]+" epsilon sigma R h rmin rmax N\n\n") + sys.exit(-1) + +epsilon = float(sys.argv[1]) +sigma = float(sys.argv[2]) +R = float(sys.argv[3]) +h = float(sys.argv[4]) +rmin = float(sys.argv[5]) +rmax = float(sys.argv[6]) +N = int(sys.argv[7]) + +subtract_Urcut = False +if len(sys.argv) == 9: + subtract_Urcut = True +rcut = rmax + +for i in range(0,N): + r = rmin + i*(rmax-rmin)/(N-1) + U_r = U(r, epsilon, sigma, R, h) + F_r = F(r, epsilon, sigma, R, h) + if subtract_Urcut: + U_r -= U(rcut, epsilon, sigma, R, h) + if (r >= rcut) or (i==N-1): + U_r = 0.0 + F_r = 0.0 + print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_dihedral_table.py b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_dihedral_table.py new file mode 100755 index 0000000000..34c66418a8 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_dihedral_table.py @@ -0,0 +1,67 @@ +#!/usr/bin/env python + +# Calculate a table of dihedral angle interactions used in the alpha-helix +# and beta-sheet regions of the frustrated protein model described in +# provided in figure 8 of the supplemental materials section of: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# Note that the "A" and "B" parameters were incorrectly reported to be +# 5.4*epsilon and 6.0*epsilon. The values used were 5.6 and 6.0 epsilon. +# The phiA and phiB values were 57.29577951308232 degrees (1 rad) +# and 180 degrees, respectively. Both expA and expB were 6.0. +# +# To generate the table used for the alpha-helix (1 degree resolution) use this: +# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 +# To generate the table used for the beta-sheets (1 degree resolution) use this: +# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360 +# +# (If you're curious as to why I set the location of the minima at phi_alpha +# to 1.0 radians (57.2957795 degrees), there was no particularly good reason. +# I think the correct value turns out to be something closer to 50 degrees.) + + +from math import * +import sys + + +# The previous version included the repulsive core term +def U(phi, A, phiA, expA, B, phiB, expB, use_radians=False): + conv_units = pi/180.0 + if use_radians: + conv_units = 1.0 + termA = pow(cos(0.5*(phi-phiA)*conv_units), expA) + termB = pow(cos(0.5*(phi-phiB)*conv_units), expB) + return -A*termA - B*termB + +# The previous version included the repulsive core term +def F(phi, A, phiA, expA, B, phiB, expB, use_radians=False): + conv_units = pi/180.0 + if use_radians: + conv_units = 1.0 + termA = (0.5*sin(0.5*(phi-phiA)*conv_units) * + expA * pow(cos(0.5*(phi-phiA)*conv_units), expA-1.0)) + termB = (0.5*sin(0.5*(phi-phiB)*conv_units) * + expB * pow(cos(0.5*(phi-phiB)*conv_units), expB-1.0)) + return -conv_units*(A*termA + B*termB) + +if len(sys.argv) != 10: + sys.stderr.write("Error: expected 9 arguments:\n" + "\n" + "Usage: "+sys.argv[0]+" A phiA expA B phiB expB phiMin phiMax N\n\n") + sys.exit(-1) + +A = float(sys.argv[1]) +phiA = float(sys.argv[2]) +expA = float(sys.argv[3]) +B = float(sys.argv[4]) +phiB = float(sys.argv[5]) +expB = float(sys.argv[6]) +phi_min = float(sys.argv[7]) +phi_max = float(sys.argv[8]) +N = int(sys.argv[9]) + +for i in range(0,N): + phi = phi_min + i*(phi_max - phi_min)/(N-1) + U_phi = U(phi, A, phiA, expA, B, phiB, expB, use_radians=False) + F_phi = F(phi, A, phiA, expA, B, phiB, expB, use_radians=False) + print(str(i+1)+' '+str(phi)+' '+str(U_phi)+' '+str(F_phi)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/minichaperone.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/minichaperone.lt new file mode 100644 index 0000000000..1d37823b7a --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/minichaperone.lt @@ -0,0 +1,41 @@ +# Here we define a trivial molecule containing only one particle. + +Minichaperone { + + # atomID molID atomType charge x y z + + write("Data Atoms") { + $atom:C $mol @atom:C 0.0 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom:C 100.0 + } + + write_once("In Settings") { + # If for some reason there are multiple chaperones present, + # I assume that they interact repulsively (hence, L=0) + + # i j pairStyle eps sig K L + + pair_coeff @atom:C @atom:C lj/charmm/coul/charmm/inter 1.0 3.0 1 0 + + # Optional: define the atoms in the "chaperonins" group: + # (Defining a group for the chaperone makes it easy to immobilize it later.) + + group chaperones type @atom:C + } + + # Specify which pair_styles, and atom styles work well with + # this model. (Again this can be overridden later.) + + write_once("In Init") { + units lj + atom_style full + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 8.0 9.0 + } + +} # Minichaperone + +# We have not specified how this particle interacts with other particles +# besides itself. Later on you must do this. diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.lt new file mode 100644 index 0000000000..8f8c37d08b --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.lt @@ -0,0 +1,72 @@ +write_once("Data Boundary") { + 0.0 80.0 xlo xhi + 0.0 80.0 ylo yhi + 0.0 80.0 zlo zhi +} + + +import "1beadFrustrated_variants.lt" +import "minichaperone.lt" + + +# Create 8 proteins and 8 chaperones (2x2x2 array): +# NOTE: Below I create multiple proteins and multiple chaperones +# to see what would happen. (I suspect nothing good. In the +# 2006 paper, only 1 protein and 1 chaperone were present.) + + +proteins = new 1beadUnfolded [2].move(40,0,0) + [2].move(0,40,0) + [2].move(0,0,40) + +chaperones = new Minichaperone [2].move(40,0,0) + [2].move(0,40,0) + [2].move(0,0,40) + +proteins[*][*][*].move(20,20,20) # to avoid overlap with the chaperones + + + +# If you only want 1 protein and 1 chaperone +# then replace the lines above with: +# +# protein = new 1beadMisfolded +# chaperone = new Minichaperone + + + + + +# ---- Now define interactions between the atoms in the protein ---- +# ---- (named "B", "L", "N") and the atom which represents the ---- +# ---- chaperone ("c"). These interactions are tabulated. ---- + +write_once("In Settings") { + pair_coeff @atom:Minichaperone/C @atom:1beadFrustrated/B table table_minichaperone_h=0.6.dat CH_H0.6 + pair_coeff @atom:Minichaperone/C @atom:1beadFrustrated/L table table_minichaperone_h=0.dat CH_H0 + pair_coeff @atom:Minichaperone/C @atom:1beadFrustrated/N table table_minichaperone_h=0.dat CH_H0 +} + +# Note: If you want purely repulsive spheres (crowding, h=0.0) +# instead of an attractive "hydrophobic" chaperone (h=0.6) +# then replace "table_minichaperone_h=0_6.dat CH_H0_6" +# with "table_minichaperone_h=0.dat CH_H0" +# (... or just use an ordinary Lennard-Jones interaction +# with sigma = 6.0 and epsilon near 0.0) + + +# LAMMPS has many available force field styles (and atom styles). Here we +# select the ones which work well for the full combine system. (This should +# override any settings made in "1beadFrustrated.lt" or "minichaperone.lt") + + +write_once("In Init") { + units lj + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid table spline 360 + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 table spline 981 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) +} diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_dihedral_frustrated.dat b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_dihedral_frustrated.dat new file mode 100644 index 0000000000..d660fee308 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_dihedral_frustrated.dat @@ -0,0 +1,735 @@ +# Table of the potential and its negative derivative for frustrated alpha helix +# (Note: Derivatives are in units of energy/radians, not energy/degrees.) +# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 + +FRUSTRATED_ALPHA +N 360 DEGREES + +1 0.0 -2.74081145103 0.0783990792662 +2 1.0 -2.81950869101 0.0789852583442 +3 2.0 -2.89876136749 0.0795096391909 +4 3.0 -2.97850675562 0.0799703813963 +5 4.0 -3.05868032959 0.0803657243943 +6 5.0 -3.13921584545 0.0806939935737 +7 6.0 -3.22004543014 0.0809536062381 +8 7.0 -3.30109967628 0.0811430773977 +9 8.0 -3.38230774267 0.0812610253741 +10 9.0 -3.46359746038 0.0813061772009 +11 10.0 -3.54489544401 0.0812773738039 +12 11.0 -3.62612720812 0.0811735749433 +13 12.0 -3.70721728841 0.0809938639029 +14 13.0 -3.78808936748 0.080737451911 +15 14.0 -3.86866640485 0.0804036822781 +16 15.0 -3.94887077101 0.0799920342374 +17 16.0 -4.02862438516 0.0795021264757 +18 17.0 -4.10784885622 0.0789337203415 +19 18.0 -4.18646562704 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-1.85985831882 0.0672956071568 +350 349.0 -1.92773877092 0.0684595158069 +351 350.0 -1.99676540616 0.0695875914917 +352 351.0 -2.06690124527 0.0706775413231 +353 352.0 -2.13810701636 0.0717270740805 +354 353.0 -2.21034115987 0.0727339066469 +355 354.0 -2.28355983986 0.0736957705223 +356 355.0 -2.35771696194 0.0746104183955 +357 356.0 -2.43276419776 0.0754756307561 +358 357.0 -2.50865101613 0.0762892225281 +359 358.0 -2.58532472075 0.0770490497051 +360 359.0 -2.66273049463 0.0777530159679 + +# Table of the potential and its negative derivative for frustrated beta sheet +# (Note: Derivatives are in units of energy/radians, not energy/degrees.) +# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360 + +FRUSTRATED_BETA +N 360 DEGREES + +1 0.0 -2.55809068762 0.0731724739818 +2 1.0 -2.63154144494 0.0737195744566 +3 2.0 -2.70551060968 0.0742089966437 +4 3.0 -2.77993963883 0.074639023134 +5 4.0 -2.85476830901 0.0750080115297 +6 5.0 -2.92993479441 0.0753144003899 +7 6.0 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a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.6.dat b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.6.dat new file mode 100644 index 0000000000..d2b1ed3aaf --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.6.dat @@ -0,0 +1,988 @@ +# Interaction between a chaperone wall and hydrophobic ("B") beads (h=0.6) +# Generated using: +# generate_tables/calc_chaperone_table.py 1.0 1.0 3.0 0.60 3.1 8.0 981 True + +CH_H0.6 +N 981 R 3.1 8.0 + +1 3.1 24321971157.7 2.4400451019e+12 +2 3.105 14907528428.0 1.42456746092e+12 +3 3.11 9347010266.92 8.52735030437e+11 +4 3.115 5983057175.03 5.22187648991e+11 +5 3.12 3902942155.05 3.26496996649e+11 +6 3.125 2590648415.38 2.0808159227e+11 +7 3.13 1747350825.1 1.34970444886e+11 +8 3.135 1196139798.89 88984974583.5 +9 3.14 830130182.341 59559787515.6 +10 3.145 583518174.975 40428507749.3 +11 3.15 415078797.287 27803974550.9 +12 3.155 298562827.719 19356989964.4 +13 3.16 217001769.743 13631486848.5 +14 3.165 159270305.159 9703243449.66 +15 3.17 117976881.962 6977184032.49 +16 3.175 88149161.6455 5064988683.98 +17 3.18 66402860.1298 3710042118.5 +18 3.185 50409022.6215 2740737360.59 +19 3.19 38548170.6708 2041021063.98 +20 3.195 29683036.1074 1531572773.33 +21 3.2 23007502.8905 1157631256.92 +22 3.205 17945109.6836 881028781.898 +23 3.21 14080149.2893 674921399.554 +24 3.215 11110438.2418 520266326.167 +25 3.22 8814639.75879 403443800.764 +26 3.225 7029455.47123 314636408.027 +27 3.23 5633571.16439 246714657.082 +28 3.235 4536265.59262 194464091.949 +29 3.24 3669265.83647 154044868.616 +30 3.245 2980881.1453 122610915.077 +31 3.25 2431748.15466 98039536.8272 +32 3.255 1991724.07297 78738058.3506 +33 3.26 1637603.46485 63504600.2322 +34 3.265 1351429.90872 51427172.534 +35 3.27 1119240.11293 41810074.9071 +36 3.275 930124.378436 34119886.2947 +37 3.28 775519.857832 27945597.578 +38 3.285 648676.115123 22969017.4933 +39 3.29 544248.919174 18942684.9889 +40 3.295 457989.984944 15673297.5619 +41 3.3 386508.875651 13009215.1485 +42 3.305 327089.446276 10830991.226 +43 3.31 277547.709074 9044163.93118 +44 3.315 236121.303553 7573742.76366 +45 3.32 201383.18845 6359973.47163 +46 3.325 172173.978278 5355070.91875 +47 3.33 147548.691578 4520688.28477 +48 3.335 126734.684289 3825948.80978 +49 3.34 109098.298235 3245909.11014 +50 3.345 94118.3261235 2760354.93052 +51 3.35 81364.827777 2352853.97713 +52 3.355 70482.1624146 2010008.31682 +53 3.36 61175.3541703 1720862.26897 +54 3.365 53199.1018261 1476431.88582 +55 3.37 46348.8930587 1269329.84244 +56 3.375 40453.7990113 1093465.44786 +57 3.38 35370.6146686 943803.998782 +58 3.385 30979.0803706 816173.162054 +59 3.39 27177.9744013 707106.743488 +60 3.395 23881.9094124 613718.268337 +61 3.4 21018.6991377 533598.403624 +62 3.405 18527.1884441 464731.50307 +63 3.41 16355.4608211 405427.532611 +64 3.415 14459.3541284 354266.400629 +65 3.42 12801.228731 310052.319542 +66 3.425 11348.9427887 271776.300627 +67 3.43 10074.9979765 238585.259865 +68 3.435 8955.82575185 209756.510836 +69 3.44 7971.18978782 184676.657916 +70 3.445 7103.68463562 162824.092297 +71 3.45 6338.31427303 143754.444665 +72 3.455 5662.13711315 127088.469763 +73 3.46 5063.9664184 112501.9356 +74 3.465 4534.11699728 99717.1686967 +75 3.47 4064.19064042 88495.970274 +76 3.475 3646.89404446 78633.6696895 +77 3.48 3275.88403311 69954.1231906 +78 3.485 2945.63575657 62305.4999784 +79 3.49 2651.33026883 55556.7252625 +80 3.495 2388.75847582 49594.4725913 +81 3.5 2154.23893796 44320.6162531 +82 3.505 1944.54741747 39650.0697323 +83 3.51 1756.8563988 35508.9486835 +84 3.515 1588.68309151 31833.0071751 +85 3.52 1437.84465949 28566.3044359 +86 3.525 1302.41961585 25660.0663588 +87 3.53 1180.71448694 23071.7118275 +88 3.535 1071.23498579 20764.0187577 +89 3.54 972.661050857 18704.4087568 +90 3.545 883.825202407 16864.3326446 +91 3.55 803.693750954 15218.7418698 +92 3.555 731.350460573 13745.6331832 +93 3.56 665.982328363 12425.6558809 +94 3.565 606.867190408 11241.7725673 +95 3.57 553.362906393 10178.9657593 +96 3.575 504.897910387 9223.98381086 +97 3.58 460.962945446 8365.12060921 +98 3.585 421.103825306 7592.02431669 +99 3.59 384.915088285 6895.53112553 +100 3.595 352.034427161 6267.5205811 +101 3.6 322.137794751 5700.78952663 +102 3.605 294.935098544 5188.94214534 +103 3.61 270.166409464 4726.29393494 +104 3.615 247.598619855 4307.78775517 +105 3.62 227.022494431 3928.92034957 +106 3.625 208.250065337 3585.67796495 +107 3.63 191.112328875 3274.47988201 +108 3.635 175.457206974 2992.12883298 +109 3.64 161.147741205 2735.76742147 +110 3.645 148.060491326 2502.83977901 +111 3.65 136.084113848 2291.05779528 +112 3.655 125.118099223 2098.37134728 +113 3.66 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-3.09346599767e-05 -0.00207982254527 +979 7.99 -2.05648617073e-05 -0.00206810960966 +980 7.995 -1.0253435891e-05 -0.00205647346771 +981 8.0 0.0 0.0 diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.dat b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.dat new file mode 100644 index 0000000000..82eaa7e158 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.dat @@ -0,0 +1,989 @@ +# Interaction between a chaperone wall and hydrophilic ("L", "N") beads (h=0.0) +# Generated using: +# generate_tables/calc_chaperone_table.py 1.0 1.0 3.0 0.00 3.1 8.0 981 True + +CH_H0 +N 981 R 3.1 8.0 + +1 3.1 24322007640.7 2.44004657299e+12 +2 3.105 14907558394.3 1.42456861215e+12 +3 3.11 9347035105.18 8.52735941633e+11 +4 3.115 5983077933.86 5.22188377701e+11 +5 3.12 3902959636.31 3.26497584961e+11 +6 3.125 2590663239.27 2.08082071378e+11 +7 3.13 1747363476.38 1.34970838198e+11 +8 3.135 1196150660.14 88985299862.7 +9 3.14 830139558.184 59560058382.9 +10 3.145 583526310.01 40428734750.9 +11 3.15 415085889.414 27804165925.8 +12 3.155 298569038.21 19357152203.7 +13 3.16 217007230.904 13631625105.8 +14 3.165 159275126.218 9703361847.17 +15 3.17 117981153.625 6977285889.84 +16 3.175 88152959.6539 5065076691.93 +17 3.18 66406248.0614 3710118471.36 +18 3.185 50412054.1061 2740803858.1 +19 3.19 38550891.1571 2041079190.29 +20 3.195 29685484.2812 1531623758.63 +21 3.2 23009711.8183 1157676125.86 +22 3.205 17947107.7408 881068391.885 +23 3.21 14081960.9175 674956471.214 +24 3.215 11112084.5698 520297467.685 +25 3.22 8816139.11379 403471527.483 +26 3.225 7030823.80219 314661158.279 +27 3.23 5634822.39381 246736805.049 +28 3.235 4537411.91017 194483958.161 +29 3.24 3670317.94503 154062728.557 +30 3.245 2981848.4679 122627006.268 +31 3.25 2432639.00923 98054064.6797 +32 3.255 1992545.82032 78751201.0309 +33 3.26 1638362.63452 63516512.707 +34 3.265 1352132.30623 51437989.9558 +35 3.27 1119890.91156 41819915.4536 +36 3.275 930728.197936 34128853.5593 +37 3.28 776080.832192 27953782.5881 +38 3.285 649197.950984 22976500.4202 +39 3.29 544734.946388 18949536.6006 +40 3.295 458443.200409 15679580.461 +41 3.3 386931.981432 13014984.83 +42 3.305 327484.882814 10836296.983 +43 3.31 277917.684205 9049049.63384 +44 3.315 236467.817902 7578247.52911 +45 3.32 201708.057716 6364132.2427 +46 3.325 172478.852825 5358914.96458 +47 3.33 147835.073691 4524245.63494 +48 3.335 127003.943407 3829244.63171 +49 3.34 109351.684422 3248966.03768 +50 3.345 94356.982001 2763193.35086 +51 3.35 81589.7991199 2355492.28163 +52 3.355 70694.4075656 2012463.12085 +53 3.36 61375.7524283 1723148.60489 +54 3.365 53388.4609277 1478563.37272 +55 3.37 46527.9558627 1271318.83571 +56 3.375 40623.2494805 1095323.17118 +57 3.38 35531.0832305 945540.660872 +58 3.385 31131.1487289 817798.059995 +59 3.39 27322.1798598 708628.354433 +60 3.395 24018.7487675 615144.330958 +61 3.4 21148.6321858 534935.990585 +62 3.405 18650.6411473 465987.08561 +63 3.41 16472.8281676 406607.038172 +64 3.415 14571.00272 355375.264352 +65 3.42 12907.4991276 311095.530355 +66 3.425 11450.1516342 272758.442538 +67 3.43 10171.439929 239510.549012 +68 3.435 9047.7752383 210628.82877 +69 3.44 8058.90260095 185499.581541 +70 3.445 7187.39938846 163600.920836 +71 3.45 6418.25372556 144488.223969 +72 3.455 5738.50938334 127782.014261 +73 3.46 5136.9660889 113157.848128 +74 3.465 4603.92612777 100337.85845 +75 3.47 4130.97969454 89083.6690543 +76 3.475 3710.8227393 79190.4466465 +77 3.48 3337.10211855 70481.8981958 +78 3.485 3004.28373073 62806.0557792 +79 3.49 2707.54003568 56031.718535 +80 3.495 2442.65394998 50045.4440029 +81 3.5 2205.93660145 44748.9996316 +82 3.505 1994.15683268 40057.2004294 +83 3.51 1804.48068152 35896.0712099 +84 3.515 1634.41934741 32201.2821773 +85 3.52 1481.78438725 28916.8150767 +86 3.525 1344.64907977 25993.8241582 +87 3.53 1221.31506159 23389.6620133 +88 3.535 1110.28347503 21067.0451721 +89 3.54 1010.22998333 18993.3383579 +90 3.545 919.9831055 17139.9396418 +91 3.55 838.505404885 15481.7515237 +92 3.555 764.877134293 13996.7253013 +93 3.56 698.281998657 12665.4680354 +94 3.565 637.994745566 11470.9030593 +95 3.57 583.370335637 10397.9763514 +96 3.575 533.834480178 9433.40224818 +97 3.58 488.875363677 8565.44294671 +98 3.585 448.036394307 7783.71706925 +99 3.59 410.909847488 7079.03325566 +100 3.595 377.131286207 6443.24533767 +101 3.6 346.374657747 5869.126147 +102 3.605 318.34798013 5350.25743201 +103 3.61 292.789543287 4880.93371692 +104 3.615 269.464560006 4456.07824337 +105 3.62 248.162210353 4071.16939457 +106 3.625 228.693030668 3722.17622503 +107 3.63 210.886604667 3405.5019084 +108 3.635 194.589519671 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7.795 5.402401468e-08 3.33222289779e-07 +941 7.8 5.23679304898e-08 3.29220126433e-07 +942 7.805 5.07317266285e-08 3.25270035737e-07 +943 7.81 4.91151445613e-08 3.21371288087e-07 +944 7.815 4.75179293742e-08 3.17523164833e-07 +945 7.82 4.59398297194e-08 3.13724958102e-07 +946 7.825 4.43805977617e-08 3.09975970624e-07 +947 7.83 4.28399891263e-08 3.06275515564e-07 +948 7.835 4.13177628469e-08 3.02622916355e-07 +949 7.84 3.98136813144e-08 2.99017506534e-07 +950 7.845 3.83275102273e-08 2.95458629582e-07 +951 7.85 3.68590185422e-08 2.91945638765e-07 +952 7.855 3.54079784251e-08 2.8847789698e-07 +953 7.86 3.39741652039e-08 2.85054776599e-07 +954 7.865 3.25573573211e-08 2.81675659322e-07 +955 7.87 3.11573362879e-08 2.78339936025e-07 +956 7.875 2.97738866382e-08 2.7504700662e-07 +957 7.88 2.84067958844e-08 2.71796279909e-07 +958 7.885 2.70558544725e-08 2.68587173443e-07 +959 7.89 2.57208557397e-08 2.65419113385e-07 +960 7.895 2.44015958707e-08 2.62291534374e-07 +961 7.9 2.30978738564e-08 2.59203879393e-07 +962 7.905 2.18094914519e-08 2.56155599635e-07 +963 7.91 2.05362531363e-08 2.53146154374e-07 +964 7.915 1.92779660724e-08 2.50175010842e-07 +965 7.92 1.8034440067e-08 2.47241644098e-07 +966 7.925 1.68054875325e-08 2.44345536912e-07 +967 7.93 1.55909234484e-08 2.41486179638e-07 +968 7.935 1.43905653237e-08 2.38663070101e-07 +969 7.94 1.32042331597e-08 2.35875713474e-07 +970 7.945 1.20317494138e-08 2.33123622171e-07 +971 7.95 1.08729389636e-08 2.30406315726e-07 +972 7.955 9.72762907123e-09 2.27723320689e-07 +973 7.96 8.59564934896e-09 2.2507417051e-07 +974 7.965 7.47683172465e-09 2.2245840544e-07 +975 7.97 6.37101040818e-09 2.19875572416e-07 +976 7.975 5.27802185823e-09 2.17325224966e-07 +977 7.98 4.19770474957e-09 2.148069231e-07 +978 7.985 3.12989994095e-09 2.12320233213e-07 +979 7.99 2.07445044336e-09 2.09864727985e-07 +980 7.995 1.03120138888e-09 2.07439986287e-07 +981 8.0 0.0 0.0 + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.min b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.min new file mode 100644 index 0000000000..e2d4a5cce4 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.min @@ -0,0 +1,24 @@ +# -- Init section -- + +include system.in.init + +# -- Atom definition section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# Optional: Make sure the pairwise energies look reasonable: +pair_write 1 4 1001 r 4.05 8 test_chap-B.dat C-B 0 0 +pair_write 2 4 1001 r 4.05 8 test_chap-L.dat C-L 0 0 +pair_write 3 4 1001 r 4.05 8 test_chap-N.dat C-N 0 0 + +# -- Run section -- + +dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz + +minimize 1.0e-5 1.0e-7 500 2000 + +write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.nvt new file mode 100644 index 0000000000..523a16575a --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.nvt @@ -0,0 +1,46 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +# I you want to be careful, you can minimize the system first. (Try using +# "run.in.min" and uncomment the read_restart command in this file below.) +# read_restart system_after_min.rst + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 0.025 +dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz + +# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". +# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) + +fix fxlan all langevin 0.25 0.25 1.0 48279 +fix fxnve all nve + +# Notes: +# The temperature is in reduced units and is set to 0.25 +# which is the folding temperature for the frustrated protein +# The inverse-damping-rate "damp" (which has units of time) is set to 1.0, +# as it was in the paper. (Hopefully folding times should be similar.) +# (See http://lammps.sandia.gov/doc/fix_langevin.html) + + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo_modify norm no #(report total energy not energy / num_atoms) +thermo 5000 #(time interval for printing out "thermo" data) + +#restart 100000000 restart_nvt + +run 1000000000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README.TXT new file mode 100644 index 0000000000..77af3de15a --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README.TXT @@ -0,0 +1,29 @@ +# This directory demonstrates how to run a short simulation of +# the "frustrated" coarse-grained protein model used in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) +# +# During this short simulation (run_short_sim.nvt.in) the protein evolves +# from an unfolded initial conformation to a misfolded conformation. +# (Visualize using VMD. Note: It can take hundreds of millions of +# timesteps to escape from this conformation and reach the folded state.) +# +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. + +------------- +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_run.sh new file mode 100755 index 0000000000..99338c7708 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_run.sh @@ -0,0 +1,21 @@ +# You would probably run lammps this way: +# +# lmp_ubuntu -i run.in.nvt + +# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer +# to the input scripts & data files you created earlier when you ran moltemplate +# system.in.init, system.in.settings, system.data + + +# ----------------------------------- + +LAMMPS_COMMAND="lmp_ubuntu" + +# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps +# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. + +# Run lammps using the following 3 commands: + +"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +"$LAMMPS_COMMAND" -i run_short_sim.in.nvt # production run + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_setup.sh new file mode 100755 index 0000000000..f2462426f1 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_setup.sh @@ -0,0 +1,24 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -overlay-dihdedrals system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + cp -r table*.dat ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 0000000000..c7f8572b29 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,85 @@ +PSF + + 1 !NTITLE + REMARKS VMD generated structure x-plor psf file + + 27 !NATOM + 1 1 2 2 0.000000 1.0000 0 + 2 1 1 1 0.000000 1.0000 0 + 3 1 2 2 0.000000 1.0000 0 + 4 1 1 1 0.000000 1.0000 0 + 5 1 2 2 0.000000 1.0000 0 + 6 1 1 1 0.000000 1.0000 0 + 7 1 3 3 0.000000 1.0000 0 + 8 1 3 3 0.000000 1.0000 0 + 9 1 1 1 0.000000 1.0000 0 + 10 1 2 2 0.000000 1.0000 0 + 11 1 1 1 0.000000 1.0000 0 + 12 1 2 2 0.000000 1.0000 0 + 13 1 1 1 0.000000 1.0000 0 + 14 1 2 2 0.000000 1.0000 0 + 15 1 3 3 0.000000 1.0000 0 + 16 1 3 3 0.000000 1.0000 0 + 17 1 3 3 0.000000 1.0000 0 + 18 1 1 1 0.000000 1.0000 0 + 19 1 1 1 0.000000 1.0000 0 + 20 1 2 2 0.000000 1.0000 0 + 21 1 2 2 0.000000 1.0000 0 + 22 1 1 1 0.000000 1.0000 0 + 23 1 1 1 0.000000 1.0000 0 + 24 1 2 2 0.000000 1.0000 0 + 25 1 2 2 0.000000 1.0000 0 + 26 1 1 1 0.000000 1.0000 0 + 27 1 2 2 0.000000 1.0000 0 + + 26 !NBOND: bonds + 1 2 2 3 3 4 4 5 + 5 6 6 7 7 8 8 9 + 9 10 10 11 11 12 12 13 + 13 14 14 15 15 16 16 17 + 17 18 18 19 19 20 20 21 + 21 22 22 23 23 24 24 25 + 25 26 26 27 + + 25 !NTHETA: angles + 13 14 15 7 8 9 6 7 8 + 16 17 18 15 16 17 2 3 4 + 4 5 6 9 10 11 11 12 13 + 14 15 16 1 2 3 3 4 5 + 10 11 12 12 13 14 25 26 27 + 5 6 7 8 9 10 17 18 19 + 18 19 20 22 23 24 21 22 23 + 19 20 21 20 21 22 23 24 25 + 24 25 26 + + 19 !NPHI: dihedrals + 1 2 3 4 2 3 4 5 + 3 4 5 6 4 5 6 7 + 8 9 10 11 9 10 11 12 + 10 11 12 13 11 12 13 14 + 12 13 14 15 15 16 17 18 + 16 17 18 19 17 18 19 20 + 18 19 20 21 19 20 21 22 + 20 21 22 23 21 22 23 24 + 22 23 24 25 23 24 25 26 + 24 25 26 27 + + 0 !NIMPHI: impropers + + + 0 !NDON: donors + + + 0 !NACC: acceptors + + + 0 !NNB + + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 + + 1 0 !NGRP + 0 0 0 + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/initial_conformation_t=0tau.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/initial_conformation_t=0tau.jpg new file mode 100644 index 0000000000..0869126bd0 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/initial_conformation_t=0tau.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/misfolded_conformation_t=1250tau.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/misfolded_conformation_t=1250tau.jpg new file mode 100644 index 0000000000..357bc780a2 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/misfolded_conformation_t=1250tau.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated.lt new file mode 100644 index 0000000000..074b55c735 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated.lt @@ -0,0 +1,216 @@ +# This file defines the "frustrated" coarse-grained protein model used in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) + + +1beadFrustrated { + + # There are 3 atom types (referred to above as B, L, and N) + # Define their masses: + + write_once("Data Masses") { + @atom:B 1.0 + @atom:L 1.0 + @atom:N 1.0 + } + + # AtomID MoleculeID AtomType Charge X Y Z + + write("Data Atoms") { + $atom:a1 $mol @atom:L 0.0 -0.92636654 -1.8409904 -2.1482679 + $atom:a2 $mol @atom:B 0.0 -0.57313354 -1.0670787 -1.6182341 + $atom:a3 $mol @atom:L 0.0 -0.85707399 -1.2358703 -0.69350966 + $atom:a4 $mol @atom:B 0.0 -0.44231274 -0.4584993 -0.23418709 + $atom:a5 $mol @atom:L 0.0 -0.75081182 -0.62868078 0.69786737 + $atom:a6 $mol @atom:B 0.0 -0.36201977 0.11619615 1.2249098 + $atom:a7 $mol @atom:N 0.0 -0.63708237 -0.15973084 2.1723919 + $atom:a8 $mol @atom:N 0.0 0.20516047 0.10417157 2.624901 + $atom:a9 $mol @atom:B 0.0 0.57223743 0.44728103 1.7695617 + $atom:a10 $mol @atom:L 0.0 0.77646279 -0.40630393 1.3168043 + $atom:a11 $mol @atom:B 0.0 0.45475664 -0.2077937 0.40045721 + $atom:a12 $mol @atom:L 0.0 0.72712495 -1.0397637 -0.087614951 + $atom:a13 $mol @atom:B 0.0 0.36971183 -0.85840501 -0.9933019 + $atom:a14 $mol @atom:L 0.0 0.74784336 -1.5700415 -1.5859217 + $atom:a15 $mol @atom:N 0.0 0.43423905 -1.2758917 -2.4853429 + $atom:a16 $mol @atom:N 0.0 0.70583191 -0.30726921 -2.4987711 + $atom:a17 $mol @atom:N 0.0 -0.091688915 0.23323014 -2.2051358 + $atom:a18 $mol @atom:B 0.0 -0.34243283 -0.035822049 -1.2644719 + $atom:a19 $mol @atom:B 0.0 0.41961247 0.18475451 -0.65971014 + $atom:a20 $mol @atom:L 0.0 0.51968465 1.1546791 -0.77877053 + $atom:a21 $mol @atom:L 0.0 -0.40827985 1.2765273 -0.52550748 + $atom:a22 $mol @atom:B 0.0 -0.368141 0.58090904 0.19152224 + $atom:a23 $mol @atom:B 0.0 0.40327249 0.86101769 0.7336255 + $atom:a24 $mol @atom:L 0.0 0.22707289 1.8326235 0.89673346 + $atom:a25 $mol @atom:L 0.0 -0.66500182 1.7285809 1.2783166 + $atom:a26 $mol @atom:B 0.0 -0.39205603 1.0475436 1.9328097 + $atom:a27 $mol @atom:L 0.0 0.25339027 1.5246265 2.5388463 + } + + # bond-ID bond-Type atom-ID atom-ID + + write("Data Bonds") { + $bond:b1 @bond:backbone $atom:a1 $atom:a2 + $bond:b2 @bond:backbone $atom:a2 $atom:a3 + $bond:b3 @bond:backbone $atom:a3 $atom:a4 + $bond:b4 @bond:backbone $atom:a4 $atom:a5 + $bond:b5 @bond:backbone $atom:a5 $atom:a6 + $bond:b6 @bond:backbone $atom:a6 $atom:a7 + $bond:b7 @bond:backbone $atom:a7 $atom:a8 + $bond:b8 @bond:backbone $atom:a8 $atom:a9 + $bond:b9 @bond:backbone $atom:a9 $atom:a10 + $bond:b10 @bond:backbone $atom:a10 $atom:a11 + $bond:b11 @bond:backbone $atom:a11 $atom:a12 + $bond:b12 @bond:backbone $atom:a12 $atom:a13 + $bond:b13 @bond:backbone $atom:a13 $atom:a14 + $bond:b14 @bond:backbone $atom:a14 $atom:a15 + $bond:b15 @bond:backbone $atom:a15 $atom:a16 + $bond:b16 @bond:backbone $atom:a16 $atom:a17 + $bond:b17 @bond:backbone $atom:a17 $atom:a18 + $bond:b18 @bond:backbone $atom:a18 $atom:a19 + $bond:b19 @bond:backbone $atom:a19 $atom:a20 + $bond:b20 @bond:backbone $atom:a20 $atom:a21 + $bond:b21 @bond:backbone $atom:a21 $atom:a22 + $bond:b22 @bond:backbone $atom:a22 $atom:a23 + $bond:b23 @bond:backbone $atom:a23 $atom:a24 + $bond:b24 @bond:backbone $atom:a24 $atom:a25 + $bond:b25 @bond:backbone $atom:a25 $atom:a26 + $bond:b26 @bond:backbone $atom:a26 $atom:a27 + } + + # (3-body) Angles are specified below + + # (4-body) Dihedrals must be defined explicitly for every quartet of atoms. + # (These interactions are not determined by atom type.) + + # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID + + write("Data Dihedrals") { + + $dihedral:d1 @dihedral:beta $atom:a1 $atom:a2 $atom:a3 $atom:a4 + $dihedral:d2 @dihedral:beta $atom:a2 $atom:a3 $atom:a4 $atom:a5 + $dihedral:d3 @dihedral:beta $atom:a3 $atom:a4 $atom:a5 $atom:a6 + $dihedral:d4 @dihedral:beta $atom:a4 $atom:a5 $atom:a6 $atom:a7 + + # Dihedral angle forces in the turn regions were switched off + # (in this model) so just I comment them out (and \ the variable names). + # \$dihedral:d5 \@dihedral:turn $atom:a5 $atom:a6 $atom:a7 $atom:a8 + # \$dihedral:d6 \@dihedral:turn $atom:a6 $atom:a7 $atom:a8 $atom:a9 + # \$dihedral:d7 \@dihedral:turn $atom:a7 $atom:a8 $atom:a9 $atom:a10 + + $dihedral:d8 @dihedral:beta $atom:a8 $atom:a9 $atom:a10 $atom:a11 + $dihedral:d9 @dihedral:beta $atom:a9 $atom:a10 $atom:a11 $atom:a12 + $dihedral:d10 @dihedral:beta $atom:a10 $atom:a11 $atom:a12 $atom:a13 + $dihedral:d11 @dihedral:beta $atom:a11 $atom:a12 $atom:a13 $atom:a14 + $dihedral:d12 @dihedral:beta $atom:a12 $atom:a13 $atom:a14 $atom:a15 + + # Dihedral angle forces in the turn regions were switched off + # (in this model) so just I comment them out (and \ the variable names). + # \$dihedral:d13 \@dihedral:turn $atom:a13 $atom:a14 $atom:a15 $atom:a16 + # \$dihedral:d14 \@dihedral:turn $atom:a14 $atom:a15 $atom:a16 $atom:a17 + + $dihedral:d15 @dihedral:alpha $atom:a15 $atom:a16 $atom:a17 $atom:a18 + $dihedral:d16 @dihedral:alpha $atom:a16 $atom:a17 $atom:a18 $atom:a19 + $dihedral:d17 @dihedral:alpha $atom:a17 $atom:a18 $atom:a19 $atom:a20 + $dihedral:d18 @dihedral:alpha $atom:a18 $atom:a19 $atom:a20 $atom:a21 + $dihedral:d19 @dihedral:alpha $atom:a19 $atom:a20 $atom:a21 $atom:a22 + $dihedral:d20 @dihedral:alpha $atom:a20 $atom:a21 $atom:a22 $atom:a23 + $dihedral:d21 @dihedral:alpha $atom:a21 $atom:a22 $atom:a23 $atom:a24 + $dihedral:d22 @dihedral:alpha $atom:a22 $atom:a23 $atom:a24 $atom:a25 + $dihedral:d23 @dihedral:alpha $atom:a23 $atom:a24 $atom:a25 $atom:a26 + $dihedral:d24 @dihedral:alpha $atom:a24 $atom:a25 $atom:a26 $atom:a27 + } + + # All consecutively bonded triplets of atoms same 3-body bond-angle + # interaction parameters. Of coarse, we could specify them all explicitly + # (as we did for the dihedrals above), but I wanted to show how to specify + # angles by atom type instead. (You can do this for dihedrals & impropers + # also.) + + # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type + + write_once("Data Angles By Type") { + @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* + } + + # (The "*" is a wildcard character. I use "*" to denote any atom-type or + # bond-type which is defined within the current namespace: 1beadFrustrated) + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 + pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0 + pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0 + pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1 + pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0 + pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0 + } + + + # 2-body (bonded) interactions: + # + # Ubond(r) = (k/2)*(r-0)^2 + # + # The corresponding command is: + # + # bond-Type bondstylename k r0 + + write_once("In Settings") { + bond_coeff @bond:backbone harmonic 100.0 1.0 + } + + # 3-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Uangle(theta) = (k/2)*(theta-theta0)^2 + # (k in kcal/mol/rad^2, theta0 in degrees) + # + # angle-Type anglestylename k theta0 + + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 13.3333333333 105.0 + } + + + # We use tabular dihedral potentials to implement the dihedral forces. + # (Actually there is a way to use Fourier series, using multiple charmm + # style dihedral interactions, but it's slower and messier.) + + write_once("In Settings") { + # style file keyword + dihedral_coeff @dihedral:alpha table table_dihedral_frustrated.dat FRUSTRATED_ALPHA + dihedral_coeff @dihedral:beta table table_dihedral_frustrated.dat FRUSTRATED_BETA + # No need to specify dihedral interactions in the turn regions. (none exist) + } + + write_once("In Settings") { + # Optional: define the atoms in the "proteins" group + group proteins type @atom:B + group proteins type @atom:L + group proteins type @atom:N + } + + # LAMMPS has many available force field styles (and atom styles). + # Here, we pick the ones which work well for this molecular model: + + write_once("In Init") { + # --- Default options for the "1BeadFrustrated" protein model --- + # --- (These can be overridden later.) --- + units lj + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid table spline 360 + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + +} # 1beadFrustrated + + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated_variants.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated_variants.lt new file mode 100644 index 0000000000..54e2de4376 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated_variants.lt @@ -0,0 +1,85 @@ +import "1beadFrustrated.lt" + + +# Alternate starting conformation (same molecule): + + +1beadMisfolded inherits 1beadFrustrated { + + # This molecule "inherits" all of its features from "1beadFrustrated". + # Here we override the atomic positions with new coordinates: + + # AtomID MoleculeID AtomType Charge X Y Z + + write("Data Atoms") { + $atom:a1 $mol @atom:L 0.0 -0.69801399 -0.22114168 -1.9464876 + $atom:a2 $mol @atom:B 0.0 -0.40921658 -0.027063664 -1.0033251 + $atom:a3 $mol @atom:L 0.0 0.10259348 0.80836418 -1.0737085 + $atom:a4 $mol @atom:B 0.0 0.25857916 1.0054984 -0.11621451 + $atom:a5 $mol @atom:L 0.0 0.8258629 1.8325549 -0.18529135 + $atom:a6 $mol @atom:B 0.0 0.91366257 2.1950317 0.74175977 + $atom:a7 $mol @atom:N 0.0 1.4399539 1.554238 1.2994409 + $atom:a8 $mol @atom:N 0.0 0.73372573 1.0161012 1.7397275 + $atom:a9 $mol @atom:B 0.0 0.26608782 0.65302497 0.94353938 + $atom:a10 $mol @atom:L 0.0 0.97442305 0.13574211 0.50586398 + $atom:a11 $mol @atom:B 0.0 0.35889617 -0.18247555 -0.1764186 + $atom:a12 $mol @atom:L 0.0 0.87151735 -0.77260824 -0.75240916 + $atom:a13 $mol @atom:B 0.0 0.047726486 -1.0530682 -1.1902704 + $atom:a14 $mol @atom:L 0.0 0.34530697 -1.7476773 -1.8393331 + $atom:a15 $mol @atom:N 0.0 0.65865186 -2.45948 -1.2167056 + $atom:a16 $mol @atom:N 0.0 -0.16534524 -2.6219442 -0.67112167 + $atom:a17 $mol @atom:N 0.0 -0.010590421 -2.2445242 0.24748633 + $atom:a18 $mol @atom:B 0.0 0.18135771 -1.2564919 0.1767523 + $atom:a19 $mol @atom:B 0.0 -0.57472665 -0.82852797 -0.27027791 + $atom:a20 $mol @atom:L 0.0 -1.3967448 -1.0516787 0.24247346 + $atom:a21 $mol @atom:L 0.0 -1.003428 -0.85642681 1.1107555 + $atom:a22 $mol @atom:B 0.0 -0.25156735 -0.3182346 0.74262946 + $atom:a23 $mol @atom:B 0.0 -0.61751956 0.30115562 0.070426493 + $atom:a24 $mol @atom:L 0.0 -1.3347934 0.83310182 0.52625934 + $atom:a25 $mol @atom:L 0.0 -0.83315257 1.270904 1.2564086 + $atom:a26 $mol @atom:B 0.0 -0.10469759 1.6988523 0.72597181 + $atom:a27 $mol @atom:L 0.0 -0.57854905 2.3367737 0.11206868 + } + +} # 1beadMisfolded + + +1beadUnfolded inherits 1beadFrustrated { + + # This molecule "inherits" all of its features from "1beadFrustrated" + # Here we override the atomic positions with new coordinates: + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0 + $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8 + $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8 + $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0 + $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0 + $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8 + $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8 + $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0 + $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0 + $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8 + $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8 + $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0 + $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0 + $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8 + $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8 + $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2 + $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2 + $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6 + $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6 + $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2 + $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2 + $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6 + $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6 + $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2 + $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2 + $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6 + $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6 + } + +} # 1beadUnfolded + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/generate_tables/calc_dihedral_table.py b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/generate_tables/calc_dihedral_table.py new file mode 100755 index 0000000000..34c66418a8 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/generate_tables/calc_dihedral_table.py @@ -0,0 +1,67 @@ +#!/usr/bin/env python + +# Calculate a table of dihedral angle interactions used in the alpha-helix +# and beta-sheet regions of the frustrated protein model described in +# provided in figure 8 of the supplemental materials section of: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# Note that the "A" and "B" parameters were incorrectly reported to be +# 5.4*epsilon and 6.0*epsilon. The values used were 5.6 and 6.0 epsilon. +# The phiA and phiB values were 57.29577951308232 degrees (1 rad) +# and 180 degrees, respectively. Both expA and expB were 6.0. +# +# To generate the table used for the alpha-helix (1 degree resolution) use this: +# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 +# To generate the table used for the beta-sheets (1 degree resolution) use this: +# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360 +# +# (If you're curious as to why I set the location of the minima at phi_alpha +# to 1.0 radians (57.2957795 degrees), there was no particularly good reason. +# I think the correct value turns out to be something closer to 50 degrees.) + + +from math import * +import sys + + +# The previous version included the repulsive core term +def U(phi, A, phiA, expA, B, phiB, expB, use_radians=False): + conv_units = pi/180.0 + if use_radians: + conv_units = 1.0 + termA = pow(cos(0.5*(phi-phiA)*conv_units), expA) + termB = pow(cos(0.5*(phi-phiB)*conv_units), expB) + return -A*termA - B*termB + +# The previous version included the repulsive core term +def F(phi, A, phiA, expA, B, phiB, expB, use_radians=False): + conv_units = pi/180.0 + if use_radians: + conv_units = 1.0 + termA = (0.5*sin(0.5*(phi-phiA)*conv_units) * + expA * pow(cos(0.5*(phi-phiA)*conv_units), expA-1.0)) + termB = (0.5*sin(0.5*(phi-phiB)*conv_units) * + expB * pow(cos(0.5*(phi-phiB)*conv_units), expB-1.0)) + return -conv_units*(A*termA + B*termB) + +if len(sys.argv) != 10: + sys.stderr.write("Error: expected 9 arguments:\n" + "\n" + "Usage: "+sys.argv[0]+" A phiA expA B phiB expB phiMin phiMax N\n\n") + sys.exit(-1) + +A = float(sys.argv[1]) +phiA = float(sys.argv[2]) +expA = float(sys.argv[3]) +B = float(sys.argv[4]) +phiB = float(sys.argv[5]) +expB = float(sys.argv[6]) +phi_min = float(sys.argv[7]) +phi_max = float(sys.argv[8]) +N = int(sys.argv[9]) + +for i in range(0,N): + phi = phi_min + i*(phi_max - phi_min)/(N-1) + U_phi = U(phi, A, phiA, expA, B, phiB, expB, use_radians=False) + F_phi = F(phi, A, phiA, expA, B, phiB, expB, use_radians=False) + print(str(i+1)+' '+str(phi)+' '+str(U_phi)+' '+str(F_phi)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/system.lt new file mode 100644 index 0000000000..a27595559e --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/system.lt @@ -0,0 +1,20 @@ +import "1beadFrustrated_variants.lt" + + +protein = new 1beadUnfolded + + + +# Note: The protein begins in an "Unfolded" conformation. If instead +# you want it to begin in the folded or misfolded conformations use: +# protein = new 1beadFrustrated # or +# protein = new 1beadMisfolded + + + +# ("27.0" is the length of the protein when maximally extended) +write_once("Data Boundary") { + 0.0 27.0 xlo xhi + 0.0 27.0 ylo yhi + 0.0 27.0 zlo zhi +} diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/table_dihedral_frustrated.dat b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/table_dihedral_frustrated.dat new file mode 100644 index 0000000000..d660fee308 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/table_dihedral_frustrated.dat @@ -0,0 +1,735 @@ +# Table of the potential and its negative derivative for frustrated alpha helix +# (Note: Derivatives are in units of energy/radians, not energy/degrees.) +# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 + +FRUSTRATED_ALPHA +N 360 DEGREES + +1 0.0 -2.74081145103 0.0783990792662 +2 1.0 -2.81950869101 0.0789852583442 +3 2.0 -2.89876136749 0.0795096391909 +4 3.0 -2.97850675562 0.0799703813963 +5 4.0 -3.05868032959 0.0803657243943 +6 5.0 -3.13921584545 0.0806939935737 +7 6.0 -3.22004543014 0.0809536062381 +8 7.0 -3.30109967628 0.0811430773977 +9 8.0 -3.38230774267 0.0812610253741 +10 9.0 -3.46359746038 0.0813061772009 +11 10.0 -3.54489544401 0.0812773738039 +12 11.0 -3.62612720812 0.0811735749433 +13 12.0 -3.70721728841 0.0809938639029 +14 13.0 -3.78808936748 0.080737451911 +15 14.0 -3.86866640485 0.0804036822781 +16 15.0 -3.94887077101 0.0799920342374 +17 16.0 -4.02862438516 0.0795021264757 +18 17.0 -4.10784885622 0.0789337203415 +19 18.0 -4.18646562704 0.0782867227197 +20 19.0 -4.26439612115 0.0775611885609 +21 20.0 -4.34156189202 0.0767573230567 +22 21.0 -4.41788477419 0.0758754834523 +23 22.0 -4.49328703609 0.0749161804868 +24 23.0 -4.56769153408 0.0738800794563 +25 24.0 -4.64102186743 0.0727680008923 +26 25.0 -4.71320253365 0.0715809208518 +27 26.0 -4.78415908407 0.0703199708131 +28 27.0 -4.85381827903 0.0689864371778 +29 28.0 -4.92210824234 0.067581760373 +30 29.0 -4.98895861476 0.0661075335571 +31 30.0 -5.05430070586 0.0645655009259 +32 31.0 -5.11806764409 0.0629575556235 +33 32.0 -5.18019452449 0.061285737258 +34 33.0 -5.24061855376 0.0595522290273 +35 34.0 -5.29927919225 0.0577593544584 +36 35.0 -5.3561182925 0.0559095737673 +37 36.0 -5.41108023395 0.0540054798439 +38 37.0 -5.46411205346 0.0520497938726 +39 38.0 -5.51516357127 0.0500453605949 +40 39.0 -5.56418751203 0.0479951432253 +41 40.0 -5.61113962059 0.0459022180302 +42 41.0 -5.65597877221 0.0437697685824 +43 42.0 -5.69866707689 0.0416010797029 +44 43.0 -5.7391699774 0.0393995311046 +45 44.0 -5.77745634094 0.0371685907508 +46 45.0 -5.81349854393 0.034911807945 +47 46.0 -5.84727254977 0.0326328061676 +48 47.0 -5.87875797937 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0.0706775413231 +353 352.0 -2.13810701636 0.0717270740805 +354 353.0 -2.21034115987 0.0727339066469 +355 354.0 -2.28355983986 0.0736957705223 +356 355.0 -2.35771696194 0.0746104183955 +357 356.0 -2.43276419776 0.0754756307561 +358 357.0 -2.50865101613 0.0762892225281 +359 358.0 -2.58532472075 0.0770490497051 +360 359.0 -2.66273049463 0.0777530159679 + +# Table of the potential and its negative derivative for frustrated beta sheet +# (Note: Derivatives are in units of energy/radians, not energy/degrees.) +# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360 + +FRUSTRATED_BETA +N 360 DEGREES + +1 0.0 -2.55809068762 0.0731724739818 +2 1.0 -2.63154144494 0.0737195744566 +3 2.0 -2.70551060968 0.0742089966437 +4 3.0 -2.77993963883 0.074639023134 +5 4.0 -2.85476830901 0.0750080115297 +6 5.0 -2.92993479441 0.0753144003899 +7 6.0 -3.00537575069 0.0755567150326 +8 7.0 -3.08102640456 0.0757335731758 +9 8.0 -3.15682064892 0.0758436903983 +10 9.0 -3.23269114341 0.075885885404 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0.0531611720525 +342 341.0 -1.32480451282 0.0544411134304 +343 342.0 -1.37987850417 0.055703842622 +344 343.0 -1.43620582346 0.0569474464963 +345 344.0 -1.49376636966 0.0581699665097 +346 345.0 -1.55253806258 0.05936940366 +347 346.0 -1.61249680493 0.0605437236497 +348 347.0 -1.67361644969 0.0616908622471 +349 348.0 -1.73586877296 0.0628087308273 +350 349.0 -1.79922345238 0.0638952220804 +351 350.0 -1.86364805137 0.0649482158688 +352 351.0 -1.92910800931 0.0659655852184 +353 352.0 -1.9955666377 0.066945202426 +354 353.0 -2.06298512258 0.0678849452658 +355 354.0 -2.13132253309 0.0687827032771 +356 355.0 -2.20053583647 0.0696363841147 +357 356.0 -2.27057991931 0.0704439199439 +358 357.0 -2.3414076153 0.0712032738621 +359 358.0 -2.41296973939 0.0719124463259 +360 359.0 -2.48521512832 0.072569481568 diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/run.in.min b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/run.in.min new file mode 100644 index 0000000000..fce9843aa8 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/run.in.min @@ -0,0 +1,19 @@ +# -- Init section -- + +include system.in.init + +# -- Atom definition section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run section -- + +dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz + +minimize 1.0e-5 1.0e-7 500 2000 + +write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/run_short_sim.in.nvt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/run_short_sim.in.nvt new file mode 100644 index 0000000000..2974c12e8a --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/run_short_sim.in.nvt @@ -0,0 +1,50 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +# I you want to be careful, you can minimize the system first. (Try using +# "run.in.min" and uncomment the read_restart command in this file below.) +# read_restart system_after_min.rst + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 0.025 +dump 1 all custom 50 traj_nvt.lammpstrj id mol type x y z ix iy iz + +# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". +# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) + +# Keep the chaperonin fixed. Only let the protein move. + +fix fxlan proteins langevin 0.25 0.25 1.0 48279 +fix fxnve proteins nve + +# Notes: +# The temperature is in reduced units and is set to 0.25 +# which is the folding temperature for the frustrated protein +# The inverse-damping-rate "damp" (which has units of time) is set to 1.0, +# as it was in the paper. (Hopefully folding times should be similar.) +# (See http://lammps.sandia.gov/doc/fix_langevin.html) + + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo_modify norm no #(report total energy not energy / num_atoms) +thermo 50 #(time interval for printing out "thermo" data) + +#restart 100000000 restart_nvt + +# Just run it long enough for it to collapse (not fold) +# (If you need to run it longer, then dump trajectory data less frequently.) +run 50000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README.TXT new file mode 100644 index 0000000000..5da41b9a8b --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README.TXT @@ -0,0 +1,32 @@ +# This directory demonstrates how to run a short simulation of +# the "unfrustrated" coarse-grained protein model used in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) +# +# In this example, the protein is placed inside a repulsive sphere +# of radius 6.0 sigma which confines its motion. +# (This sphere is sometimes called the "chaperonin", because +# we were using it to model the crude behavior of a chaperonin cavity.) +# +# During this short simulation (run.in.nvt) the protein evolves +# from an unfolded initial conformation to the folded state. +# +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. + +------------- +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_run.sh new file mode 100755 index 0000000000..45bd2d451d --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_run.sh @@ -0,0 +1,31 @@ +# You would probably run lammps this way: +# +# lmp_ubuntu -i run.in.nvt + +# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer +# to the input scripts & data files you created earlier when you ran moltemplate +# system.in.init, system.in.settings, system.data + + + + +# ----------------------------------- + + + +LAMMPS_COMMAND="lmp_ubuntu" + +# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps +# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. + +# Run lammps using the following 3 commands: + +"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +"$LAMMPS_COMMAND" -i run.in.nvt # production run + +# Alternately, if you have MPI installed, try something like this: + +#NUMPROCS=4 +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_setup.sh new file mode 100755 index 0000000000..f2462426f1 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_setup.sh @@ -0,0 +1,24 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -overlay-dihdedrals system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + cp -r table*.dat ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 0000000000..7763505c0d --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,98 @@ +PSF + + 1 !NTITLE + REMARKS VMD generated structure x-plor psf file + + 28 !NATOM + 1 1 1 1 0.000000 100.0000 0 + 2 2 3 3 0.000000 1.0000 0 + 3 2 2 2 0.000000 1.0000 0 + 4 2 3 3 0.000000 1.0000 0 + 5 2 2 2 0.000000 1.0000 0 + 6 2 3 3 0.000000 1.0000 0 + 7 2 2 2 0.000000 1.0000 0 + 8 2 4 4 0.000000 1.0000 0 + 9 2 4 4 0.000000 1.0000 0 + 10 2 2 2 0.000000 1.0000 0 + 11 2 3 3 0.000000 1.0000 0 + 12 2 2 2 0.000000 1.0000 0 + 13 2 3 3 0.000000 1.0000 0 + 14 2 2 2 0.000000 1.0000 0 + 15 2 3 3 0.000000 1.0000 0 + 16 2 4 4 0.000000 1.0000 0 + 17 2 4 4 0.000000 1.0000 0 + 18 2 4 4 0.000000 1.0000 0 + 19 2 2 2 0.000000 1.0000 0 + 20 2 2 2 0.000000 1.0000 0 + 21 2 3 3 0.000000 1.0000 0 + 22 2 3 3 0.000000 1.0000 0 + 23 2 2 2 0.000000 1.0000 0 + 24 2 2 2 0.000000 1.0000 0 + 25 2 3 3 0.000000 1.0000 0 + 26 2 3 3 0.000000 1.0000 0 + 27 2 2 2 0.000000 1.0000 0 + 28 2 3 3 0.000000 1.0000 0 + + 26 !NBOND: bonds + 2 3 3 4 4 5 5 6 + 6 7 7 8 8 9 9 10 + 10 11 11 12 12 13 13 14 + 14 15 15 16 16 17 17 18 + 18 19 19 20 20 21 21 22 + 22 23 23 24 24 25 25 26 + 26 27 27 28 + + 25 !NTHETA: angles + 3 4 5 5 6 7 10 11 12 + 12 13 14 8 9 10 7 8 9 + 17 18 19 19 20 21 23 24 25 + 22 23 24 2 3 4 4 5 6 + 11 12 13 13 14 15 26 27 28 + 15 16 17 6 7 8 9 10 11 + 14 15 16 18 19 20 20 21 22 + 21 22 23 24 25 26 25 26 27 + 16 17 18 + + 43 !NPHI: dihedrals + 2 3 4 5 2 3 4 5 + 3 4 5 6 3 4 5 6 + 4 5 6 7 4 5 6 7 + 5 6 7 8 5 6 7 8 + 6 7 8 9 7 8 9 10 + 8 9 10 11 9 10 11 12 + 9 10 11 12 10 11 12 13 + 10 11 12 13 11 12 13 14 + 11 12 13 14 12 13 14 15 + 12 13 14 15 13 14 15 16 + 13 14 15 16 14 15 16 17 + 15 16 17 18 16 17 18 19 + 16 17 18 19 17 18 19 20 + 17 18 19 20 18 19 20 21 + 18 19 20 21 19 20 21 22 + 19 20 21 22 20 21 22 23 + 20 21 22 23 21 22 23 24 + 21 22 23 24 22 23 24 25 + 22 23 24 25 23 24 25 26 + 23 24 25 26 24 25 26 27 + 24 25 26 27 25 26 27 28 + 25 26 27 28 + + 0 !NIMPHI: impropers + + + 0 !NDON: donors + + + 0 !NACC: acceptors + + + 0 !NNB + + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 + + 1 0 !NGRP + 0 0 0 + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=0tau_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=0tau_LR.jpg new file mode 100644 index 0000000000..a0da344db5 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=0tau_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=105tau_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=105tau_LR.jpg new file mode 100644 index 0000000000..a1aa5bd855 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=105tau_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated.lt new file mode 100644 index 0000000000..0dc1f5dd05 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated.lt @@ -0,0 +1,255 @@ +# This file defines a pair of coarse-grained protein models used in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) + + +1beadUnfrustrated { + + # Note: the "unfrustrated" model is kind of funny looking. (My apologies.) + + # There are 3 atom types (referred to above as B, L, and N) + # Define their masses: + + write_once("Data Masses") { + @atom:B 1.0 + @atom:L 1.0 + @atom:N 1.0 + } + + # AtomID MoleculeID AtomType Charge X Y Z + + write("Data Atoms") { + $atom:a1 $mol @atom:L 0.0 -1.3969548 1.7525716 -0.28565118 + $atom:a2 $mol @atom:B 0.0 -0.66847917 1.0738923 -0.39651074 + $atom:a3 $mol @atom:L 0.0 -0.16610379 1.0893417 0.44519456 + $atom:a4 $mol @atom:B 0.0 0.42244126 0.35006314 0.15979926 + $atom:a5 $mol @atom:L 0.0 1.2844393 0.55103218 0.64505356 + $atom:a6 $mol @atom:N 0.0 1.9703715 0.37775946 -0.05267634 + $atom:a7 $mol @atom:N 0.0 2.574926 -0.30399114 0.34330503 + $atom:a8 $mol @atom:N 0.0 2.029546 -1.1256647 0.19829852 + $atom:a9 $mol @atom:B 0.0 1.0936146 -0.76054936 0.1043528 + $atom:a10 $mol @atom:L 0.0 0.74888247 -0.81165991 1.0334863 + $atom:a11 $mol @atom:B 0.0 -0.069536333 -0.26815389 0.94356636 + $atom:a12 $mol @atom:L 0.0 -0.65671052 -0.522532 1.7113065 + $atom:a13 $mol @atom:N 0.0 -1.5278507 -0.10774689 1.4611921 + $atom:a14 $mol @atom:L 0.0 -2.1958878 -0.8403146 1.5521738 + $atom:a15 $mol @atom:N 0.0 -2.6058074 -0.86553455 0.64397232 + $atom:a16 $mol @atom:N 0.0 -1.8447588 -1.1286421 0.042924693 + $atom:a17 $mol @atom:N 0.0 -1.5328721 -0.28576244 -0.40564841 + $atom:a18 $mol @atom:B 0.0 -0.69593879 0.027664412 0.064884008 + $atom:a19 $mol @atom:B 0.0 0.0026517494 -0.66355162 -0.11470678 + $atom:a20 $mol @atom:L 0.0 -0.35479285 -1.2282381 -0.86455878 + $atom:a21 $mol @atom:L 0.0 -0.60202976 -0.47829758 -1.4411001 + $atom:a22 $mol @atom:B 0.0 -0.14616501 0.20157397 -0.87098365 + $atom:a23 $mol @atom:B 0.0 0.7755198 -0.14153019 -0.76838748 + $atom:a24 $mol @atom:L 0.0 1.2465693 0.19738595 -1.5794731 + $atom:a25 $mol @atom:L 0.0 0.77604792 1.0612244 -1.637442 + $atom:a26 $mol @atom:B 0.0 0.44801303 1.1110219 -0.6900789 + $atom:a27 $mol @atom:L 0.0 1.0908651 1.7386382 -0.24229241 + } + + # bond-ID bond-Type atom-ID atom-ID + + write("Data Bonds") { + $bond:b1 @bond:backbone $atom:a1 $atom:a2 + $bond:b2 @bond:backbone $atom:a2 $atom:a3 + $bond:b3 @bond:backbone $atom:a3 $atom:a4 + $bond:b4 @bond:backbone $atom:a4 $atom:a5 + $bond:b5 @bond:backbone $atom:a5 $atom:a6 + $bond:b6 @bond:backbone $atom:a6 $atom:a7 + $bond:b7 @bond:backbone $atom:a7 $atom:a8 + $bond:b8 @bond:backbone $atom:a8 $atom:a9 + $bond:b9 @bond:backbone $atom:a9 $atom:a10 + $bond:b10 @bond:backbone $atom:a10 $atom:a11 + $bond:b11 @bond:backbone $atom:a11 $atom:a12 + $bond:b12 @bond:backbone $atom:a12 $atom:a13 + $bond:b13 @bond:backbone $atom:a13 $atom:a14 + $bond:b14 @bond:backbone $atom:a14 $atom:a15 + $bond:b15 @bond:backbone $atom:a15 $atom:a16 + $bond:b16 @bond:backbone $atom:a16 $atom:a17 + $bond:b17 @bond:backbone $atom:a17 $atom:a18 + $bond:b18 @bond:backbone $atom:a18 $atom:a19 + $bond:b19 @bond:backbone $atom:a19 $atom:a20 + $bond:b20 @bond:backbone $atom:a20 $atom:a21 + $bond:b21 @bond:backbone $atom:a21 $atom:a22 + $bond:b22 @bond:backbone $atom:a22 $atom:a23 + $bond:b23 @bond:backbone $atom:a23 $atom:a24 + $bond:b24 @bond:backbone $atom:a24 $atom:a25 + $bond:b25 @bond:backbone $atom:a25 $atom:a26 + $bond:b26 @bond:backbone $atom:a26 $atom:a27 + } + + # (3-body) Angles are specified below + + # (4-body) Dihedrals must be defined explicitly for every quartet of atoms. + # (These interactions are not determined by atom type.) + # + # Note that some quartets of atoms are listed because their + # potentials contain multiple terms in the Fourier expansion. + # (IE. multiple cosines... Be sure to use "-overlay-dihedrals"!) + # + # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID + + write("Data Dihedrals") { + $dihedral:d1a @dihedral:beta1 $atom:a1 $atom:a2 $atom:a3 $atom:a4 + $dihedral:d1b @dihedral:beta2 $atom:a1 $atom:a2 $atom:a3 $atom:a4 + $dihedral:d2a @dihedral:beta1 $atom:a2 $atom:a3 $atom:a4 $atom:a5 + $dihedral:d2b @dihedral:beta2 $atom:a2 $atom:a3 $atom:a4 $atom:a5 + $dihedral:d3a @dihedral:beta1 $atom:a3 $atom:a4 $atom:a5 $atom:a6 + $dihedral:d3b @dihedral:beta2 $atom:a3 $atom:a4 $atom:a5 $atom:a6 + $dihedral:d4a @dihedral:beta1 $atom:a4 $atom:a5 $atom:a6 $atom:a7 + $dihedral:d4b @dihedral:beta2 $atom:a4 $atom:a5 $atom:a6 $atom:a7 + $dihedral:d5 @dihedral:turn1 $atom:a5 $atom:a6 $atom:a7 $atom:a8 + $dihedral:d6 @dihedral:turn2 $atom:a6 $atom:a7 $atom:a8 $atom:a9 + $dihedral:d7 @dihedral:turn3 $atom:a7 $atom:a8 $atom:a9 $atom:a10 + $dihedral:d8a @dihedral:beta1 $atom:a8 $atom:a9 $atom:a10 $atom:a11 + $dihedral:d8b @dihedral:beta2 $atom:a8 $atom:a9 $atom:a10 $atom:a11 + $dihedral:d9a @dihedral:beta1 $atom:a9 $atom:a10 $atom:a11 $atom:a12 + $dihedral:d9b @dihedral:beta2 $atom:a9 $atom:a10 $atom:a11 $atom:a12 + $dihedral:d10a @dihedral:beta1 $atom:a10 $atom:a11 $atom:a12 $atom:a13 + $dihedral:d10b @dihedral:beta2 $atom:a10 $atom:a11 $atom:a12 $atom:a13 + $dihedral:d11a @dihedral:beta1 $atom:a11 $atom:a12 $atom:a13 $atom:a14 + $dihedral:d11b @dihedral:beta2 $atom:a11 $atom:a12 $atom:a13 $atom:a14 + $dihedral:d12a @dihedral:beta1 $atom:a12 $atom:a13 $atom:a14 $atom:a15 + $dihedral:d12b @dihedral:beta2 $atom:a12 $atom:a13 $atom:a14 $atom:a15 + $dihedral:d13 @dihedral:turn4 $atom:a13 $atom:a14 $atom:a15 $atom:a16 + $dihedral:d14 @dihedral:turn5 $atom:a14 $atom:a15 $atom:a16 $atom:a17 + $dihedral:d15a @dihedral:alpha1 $atom:a15 $atom:a16 $atom:a17 $atom:a18 + $dihedral:d15b @dihedral:alpha2 $atom:a15 $atom:a16 $atom:a17 $atom:a18 + $dihedral:d16a @dihedral:alpha1 $atom:a16 $atom:a17 $atom:a18 $atom:a19 + $dihedral:d16b @dihedral:alpha2 $atom:a16 $atom:a17 $atom:a18 $atom:a19 + $dihedral:d17a @dihedral:alpha1 $atom:a17 $atom:a18 $atom:a19 $atom:a20 + $dihedral:d17b @dihedral:alpha2 $atom:a17 $atom:a18 $atom:a19 $atom:a20 + $dihedral:d18a @dihedral:alpha1 $atom:a18 $atom:a19 $atom:a20 $atom:a21 + $dihedral:d18b @dihedral:alpha2 $atom:a18 $atom:a19 $atom:a20 $atom:a21 + $dihedral:d19a @dihedral:alpha1 $atom:a19 $atom:a20 $atom:a21 $atom:a22 + $dihedral:d19b @dihedral:alpha2 $atom:a19 $atom:a20 $atom:a21 $atom:a22 + $dihedral:d20a @dihedral:alpha1 $atom:a20 $atom:a21 $atom:a22 $atom:a23 + $dihedral:d20b @dihedral:alpha2 $atom:a20 $atom:a21 $atom:a22 $atom:a23 + $dihedral:d21a @dihedral:alpha1 $atom:a21 $atom:a22 $atom:a23 $atom:a24 + $dihedral:d21b @dihedral:alpha2 $atom:a21 $atom:a22 $atom:a23 $atom:a24 + $dihedral:d22a @dihedral:alpha1 $atom:a22 $atom:a23 $atom:a24 $atom:a25 + $dihedral:d22b @dihedral:alpha2 $atom:a22 $atom:a23 $atom:a24 $atom:a25 + $dihedral:d23a @dihedral:alpha1 $atom:a23 $atom:a24 $atom:a25 $atom:a26 + $dihedral:d23b @dihedral:alpha2 $atom:a23 $atom:a24 $atom:a25 $atom:a26 + $dihedral:d24a @dihedral:alpha1 $atom:a24 $atom:a25 $atom:a26 $atom:a27 + $dihedral:d24b @dihedral:alpha2 $atom:a24 $atom:a25 $atom:a26 $atom:a27 + } + + # All consecutively bonded triplets of atoms same 3-body bond-angle + # interaction parameters. Of coarse, we could specify them all explicitly + # (as we did for the dihedrals above), but I wanted to show how to specify + # angles by atom type instead. (You can do this for dihedrals & impropers + # also.) + + # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type + + write_once("Data Angles By Type") { + @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* + } + + # (The "*" is a wildcard character. I use "*" to denote any atom-type or + # bond-type which is defined within the current namespace: 1beadUnfrustrated) + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 + pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0 + pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0 + pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1 + pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0 + pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0 + } + + + # 2-body (bonded) interactions: + # + # Ubond(r) = (k/2)*(r-0)^2 + # + # The corresponding command is: + # + # bond-Type bondstylename k r0 + + write_once("In Settings") { + bond_coeff @bond:backbone harmonic 100.0 1.0 + } + + # 3-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Uangle(theta) = (k/2)*(theta-theta0)^2 + # (k in kcal/mol/rad^2, theta0 in degrees) + # + # angle-Type anglestylename k theta0 + + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 13.3333333333 105.0 + } + + # 4-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Udihedral(phi) = K * (1 + cos(n*phi - d)) + # + # The d parameter is in degrees, K is in kcal/mol/rad^2. + # + # The corresponding command is: + # + # dihedral_coeff dihedralType dihedralstylename K n d w + # ("w" is the weight for 1-4 pair interactions, which we set to 0) + + # NOTE: Currently, dihedral_coeff charmm does not allow non-integer d + # parameters. I'm hoping this will be fixed eventually. + + write_once("In Settings") { + # Correct version: + #dihedral_coeff @dihedral:alpha1 charmm -1.5 1 57.2957795 0.0 + # Replacing with + dihedral_coeff @dihedral:alpha1 charmm -1.5 1 57 0.0 + # Correct version: + #dihedral_coeff @dihedral:alpha2 charmm 0.375 2 114.591559 0.0 + # Replacing with + dihedral_coeff @dihedral:alpha2 charmm 0.375 2 115 0.0 + dihedral_coeff @dihedral:beta1 charmm -1.5 1 180 0.0 + dihedral_coeff @dihedral:beta2 charmm 0.375 2 360 0.0 + dihedral_coeff @dihedral:turn1 charmm -3.0 1 90 0.0 + # Correct version: + # dihedral_coeff @dihedral:turn2 charmm -3.0 1 11.4591559 0.0 + # Replacing with + dihedral_coeff @dihedral:turn2 charmm -3.0 1 11 0.0 + dihedral_coeff @dihedral:turn3 charmm -3.0 1 -90 0.0 + dihedral_coeff @dihedral:turn4 charmm 0.0 1 0 0.0 + dihedral_coeff @dihedral:turn5 charmm 0.0 1 0 0.0 + } + + write_once("In Settings") { + # Optional: define the atoms in the "proteins" group + group proteins type @atom:B + group proteins type @atom:L + group proteins type @atom:N + } + + # LAMMPS has many available force field styles (and atom styles). + # Here, we pick the ones which work well for this molecular model: + + write_once("In Init") { + # --- Default options for the "1BeadUnfrustrated" protein model --- + # --- (These can be overridden later.) --- + units lj + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid charmm + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + +} # 1beadUnfrustrated + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated_variants.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated_variants.lt new file mode 100644 index 0000000000..cbc8fe217c --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated_variants.lt @@ -0,0 +1,45 @@ +import "1beadUnfrustrated.lt" + + +# Alternate starting conformation (same molecule): + + +1beadUnfolded inherits 1beadUnfrustrated { + + # This molecule "inherits" all of its features from "1beadUnfrustrated" + # Here we override the atomic positions with new coordinates: + + # AtomID MoleculeID AtomType Charge X Y Z + + write("Data Atoms") { + $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0 + $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8 + $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8 + $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0 + $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0 + $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8 + $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8 + $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0 + $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0 + $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8 + $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8 + $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0 + $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0 + $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8 + $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8 + $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2 + $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2 + $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6 + $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6 + $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2 + $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2 + $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6 + $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6 + $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2 + $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2 + $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6 + $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6 + } + +} # 1beadUnfolded + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/chaperonin.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/chaperonin.lt new file mode 100644 index 0000000000..8266d2a898 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/chaperonin.lt @@ -0,0 +1,41 @@ +# Here we define a trivial molecule containing only one particle. + +Chaperonin { + + # atomID molID atomType charge x y z + + write("Data Atoms") { + $atom:C $mol @atom:C 0.0 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom:C 100.0 + } + + write_once("In Settings") { + # If for some reason there are multiple chaperones present, + # I assume that they interact repulsively (hence, L=0) + # i j epsilon sigma K L + + pair_coeff @atom:C @atom:C lj/charmm/coul/charmm/inter 1.0 6.0 1 0 + + # Optional: define the atoms in the "chaperonins" group: + # (Defining a group for the chaperone makes it easy to immobilize it later.) + + group chaperonins type @atom:C + } + + + # Specify which pair_styles, and atom styles work well with + # this model. (Again this can be overridden later.) + + write_once("In Init") { + units lj + atom_style full + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 11.0 12.0 + } + +} # Chaperonin + +# We have not specified how this particle interacts with other particles +# besides itself. Later on you must do this. diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py new file mode 100755 index 0000000000..9b86809cc3 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py @@ -0,0 +1,87 @@ +#!/usr/bin/env python + +# Calculate a table of pairwise energies and forces between atoms in the +# protein and a chaperone provided in the supplemental materials section of: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# This is stored in a tabulated force field with a singularity at a distance R. +# +# To calculate the table for interaction between +# ...the chaperone and a hydrophobic bead (2004 PNAS paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 6.0 0.475 0.0 5.9 1181 +# ...the chaperone and a hydrophilic bead (2004 PNAS paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 6.0 0.0 0.0 5.9 1181 +# ...the chaperone and a hydrophobic bead (2006 JMB paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 3.0 0.60 3.1 8.0 981 True +# ...the chaperone and a hydrophilic bead (2006 JMB paper), use this table: +# ./calc_chaperone_table.py 1.0 1.0 3.0 0.0 3.1 8.0 981 True + +from math import * +import sys + +def U(r, eps, sigma, R, h): + #print('r='+str(r)+' eps='+str(eps)+' s='+str(sigma)+' R='+str(R)+' h='+str(h)) + # Formula is undefined at r=0, but you can take the limit: + if r <= 0: + return 4.0*pi*R*R*4.0*eps*(pow((sigma/R), 12.0) + - h*pow((sigma/R), 6.0)) + xp = sigma/(r+R) + xm = sigma/(r-R) + term10 = pow(xm, 10.0) - pow(xp, 10.0) + term4 = pow(xm, 4.0) - pow(xp, 4.0) + return 4.0*pi*eps*(R/r) * (0.2*term10 - 0.5*h*term4) + +def F(r, eps, sigma, R, h): + # Formula is undefined at r=0, but you can take the limit: + if r <= 0: + return 0.0 + product_term_a = U(r, eps, sigma, R, h) / r + ixp = (r+R)/sigma + ixm = (r-R)/sigma + dix_dr = 1.0/sigma + term10 = (10.0/sigma)*(pow(ixm, -11.0) - pow(ixp, -11.0)) + term4 = (4.0/sigma)*(pow(ixm, -5.0) - pow(ixp, -5.0)) + product_term_b = 4.0*eps*pi*(R/r) * (0.2*term10 - 0.5*h*term4) + return product_term_a + product_term_b + + +class InputError(Exception): + """ A generic exception object containing a string for error reporting. + + """ + def __init__(self, err_msg): + self.err_msg = err_msg + def __str__(self): + return self.err_msg + def __repr__(self): + return str(self) + +if len(sys.argv) < 8: + sys.stderr.write("Error: expected 7 arguments:\n" + "\n" + "Usage: "+sys.argv[0]+" epsilon sigma R h rmin rmax N\n\n") + sys.exit(-1) + +epsilon = float(sys.argv[1]) +sigma = float(sys.argv[2]) +R = float(sys.argv[3]) +h = float(sys.argv[4]) +rmin = float(sys.argv[5]) +rmax = float(sys.argv[6]) +N = int(sys.argv[7]) + +subtract_Urcut = False +if len(sys.argv) == 9: + subtract_Urcut = True +rcut = rmax + +for i in range(0,N): + r = rmin + i*(rmax-rmin)/(N-1) + U_r = U(r, epsilon, sigma, R, h) + F_r = F(r, epsilon, sigma, R, h) + if subtract_Urcut: + U_r -= U(rcut, epsilon, sigma, R, h) + if (r >= rcut) or (i==N-1): + U_r = 0.0 + F_r = 0.0 + print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/system.lt new file mode 100644 index 0000000000..d8781c26f5 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/system.lt @@ -0,0 +1,45 @@ +write_once("Data Boundary") { + 0.0 20.0 xlo xhi + 0.0 20.0 ylo yhi + 0.0 20.0 zlo zhi +} + + +import "chaperonin.lt" +import "1beadUnfrustrated_variants.lt" + + +chaperinin = new Chaperonin # (hollow chaperonin, encloses protein) +protein = new 1beadUnfolded # (unfolded conformation, unfrustrated protein) + + + +# Now define interactions between the "c" atom in the +# chaperone and the "B", "L", "N" atoms in the protein: + +write_once("In Settings") { + pair_coeff @atom:Chaperonin/C @atom:1beadUnfrustrated/B table table_chaperonin_h=0.dat CH_H0 + pair_coeff @atom:Chaperonin/C @atom:1beadUnfrustrated/L table table_chaperonin_h=0.dat CH_H0 + pair_coeff @atom:Chaperonin/C @atom:1beadUnfrustrated/N table table_chaperonin_h=0.dat CH_H0 + # Note: In this example, the chaperone is playing the role of a repulsive wall + # (confinement). To use a sticky chaperonin, replace the first line with this: + # pair_coeff @atom:Chaperonin/C @atom:1beadUnfrustrated/B table table_chaperonin_h=0.475.dat CH_H0.475 +} + + + +# LAMMPS has many available force field styles (and atom styles). +# Here, we pick the ones which work well for this molecular model: + +write_once("In Init") { + # --- Default options for the "1BeadUnfrustrated" protein model --- + # --- (These can be overridden later.) --- + units lj + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid charmm + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 table spline 1181 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) +} diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat new file mode 100644 index 0000000000..675d228a90 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat @@ -0,0 +1,1188 @@ +# Interaction between a chaperonin wall and hydrophobic ("B") beads (h=0.475). +# LAMMPS would crash unless I set the minimum radius to a positive value (not 0) + +CH_H0.475 +N 1181 R 0.00000000001 5.9 + +1 0.00000000001 -0.018422088583 0.0 +2 0.005 -0.0184221525389 2.55824082873e-05 +3 0.01 -0.0184223444081 5.11654127471e-05 +4 0.015 -0.018422664195 7.67496107175e-05 +5 0.02 -0.0184231119071 0.000102335598797 +6 0.025 -0.018423687555 0.000127923973785 +7 0.03 -0.0184243911519 0.000153515332637 +8 0.035 -0.0184252227143 0.000179110272379 +9 0.04 -0.0184261822615 0.000204709390236 +10 0.045 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b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat new file mode 100644 index 0000000000..2ad6d7b691 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat @@ -0,0 +1,1187 @@ +# Interaction between a chaperonin wall and hydrophilic beads (type L or N, h=0) + +CH_H0 +N 1181 R 0.00000000001 5.9 + +1 0.00000000001 8.31299178857e-07 0.0 +2 0.005 8.31311879342e-07 -5.08022586688e-09 +3 0.01 8.31349981758e-07 -1.01608369733e-08 +4 0.015 8.31413488996e-07 -1.52422186449e-08 +5 0.02 8.31502405871e-07 -2.03247562721e-08 +6 0.025 8.31616739127e-07 -2.54088353865e-08 +7 0.03 8.31756497437e-07 -3.04948417048e-08 +8 0.035 8.319216914e-07 -3.55831611709e-08 +9 0.04 8.32112333547e-07 -4.06741800058e-08 +10 0.045 8.32328438343e-07 -4.57682847516e-08 +11 0.05 8.32570022183e-07 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-2.55154000294e+12 + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.min b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.min new file mode 100644 index 0000000000..fce9843aa8 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.min @@ -0,0 +1,19 @@ +# -- Init section -- + +include system.in.init + +# -- Atom definition section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run section -- + +dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz + +minimize 1.0e-5 1.0e-7 500 2000 + +write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.nvt new file mode 100644 index 0000000000..5fb8d71b39 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.nvt @@ -0,0 +1,48 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +# I you want to be careful, you can minimize the system first. (Try using +# "run.in.min" and uncomment the read_restart command in this file below.) +# read_restart system_after_min.rst + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 0.025 +dump 1 all custom 50 traj_nvt.lammpstrj id mol type x y z ix iy iz + +# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". +# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) + +# Keep the chaperonin fixed. Only let the protein move. + +fix fxlan proteins langevin 0.39 0.39 1.0 48279 +fix fxnve proteins nve + +# Notes: +# The temperature is in reduced units and is set to 0.39 +# which is the folding temperature for the unfrustrated protein. +# The inverse-damping-rate "damp" (which has units of time) is set to 1.0, +# as it was in the paper. (Hopefully folding times should be similar.) +# (See http://lammps.sandia.gov/doc/fix_langevin.html) + + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo_modify norm no #(report total energy not energy / num_atoms) +thermo 50 #(time interval for printing out "thermo" data) + +#restart 100000000 restart_nvt + +run 5000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README.TXT new file mode 100644 index 0000000000..b2770e3e3d --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README.TXT @@ -0,0 +1,27 @@ +# This directory demonstrates how to run a short simulation of +# the "unfrustrated" coarse-grained protein model used in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) +# +# During this short simulation (run.in.nvt) the protein evolves +# from an unfolded initial conformation to the folded state. +# +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. + +------------- +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_run.sh new file mode 100755 index 0000000000..45bd2d451d --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_run.sh @@ -0,0 +1,31 @@ +# You would probably run lammps this way: +# +# lmp_ubuntu -i run.in.nvt + +# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer +# to the input scripts & data files you created earlier when you ran moltemplate +# system.in.init, system.in.settings, system.data + + + + +# ----------------------------------- + + + +LAMMPS_COMMAND="lmp_ubuntu" + +# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps +# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. + +# Run lammps using the following 3 commands: + +"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +"$LAMMPS_COMMAND" -i run.in.nvt # production run + +# Alternately, if you have MPI installed, try something like this: + +#NUMPROCS=4 +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_setup.sh new file mode 100755 index 0000000000..cb3196cf8a --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_setup.sh @@ -0,0 +1,23 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -overlay-dihdedrals system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 0000000000..1470af4bc1 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,97 @@ +PSF + + 1 !NTITLE + REMARKS VMD generated structure x-plor psf file + + 27 !NATOM + 1 1 2 2 0.000000 1.0000 0 + 2 1 1 1 0.000000 1.0000 0 + 3 1 2 2 0.000000 1.0000 0 + 4 1 1 1 0.000000 1.0000 0 + 5 1 2 2 0.000000 1.0000 0 + 6 1 1 1 0.000000 1.0000 0 + 7 1 3 3 0.000000 1.0000 0 + 8 1 3 3 0.000000 1.0000 0 + 9 1 1 1 0.000000 1.0000 0 + 10 1 2 2 0.000000 1.0000 0 + 11 1 1 1 0.000000 1.0000 0 + 12 1 2 2 0.000000 1.0000 0 + 13 1 1 1 0.000000 1.0000 0 + 14 1 2 2 0.000000 1.0000 0 + 15 1 3 3 0.000000 1.0000 0 + 16 1 3 3 0.000000 1.0000 0 + 17 1 3 3 0.000000 1.0000 0 + 18 1 1 1 0.000000 1.0000 0 + 19 1 1 1 0.000000 1.0000 0 + 20 1 2 2 0.000000 1.0000 0 + 21 1 2 2 0.000000 1.0000 0 + 22 1 1 1 0.000000 1.0000 0 + 23 1 1 1 0.000000 1.0000 0 + 24 1 2 2 0.000000 1.0000 0 + 25 1 2 2 0.000000 1.0000 0 + 26 1 1 1 0.000000 1.0000 0 + 27 1 2 2 0.000000 1.0000 0 + + 26 !NBOND: bonds + 1 2 2 3 3 4 4 5 + 5 6 6 7 7 8 8 9 + 9 10 10 11 11 12 12 13 + 13 14 14 15 15 16 16 17 + 17 18 18 19 19 20 20 21 + 21 22 22 23 23 24 24 25 + 25 26 26 27 + + 25 !NTHETA: angles + 13 14 15 7 8 9 6 7 8 + 16 17 18 15 16 17 2 3 4 + 4 5 6 9 10 11 11 12 13 + 14 15 16 1 2 3 3 4 5 + 10 11 12 12 13 14 25 26 27 + 5 6 7 8 9 10 17 18 19 + 18 19 20 22 23 24 21 22 23 + 19 20 21 20 21 22 23 24 25 + 24 25 26 + + 43 !NPHI: dihedrals + 1 2 3 4 1 2 3 4 + 2 3 4 5 2 3 4 5 + 3 4 5 6 3 4 5 6 + 4 5 6 7 4 5 6 7 + 5 6 7 8 6 7 8 9 + 7 8 9 10 8 9 10 11 + 8 9 10 11 9 10 11 12 + 9 10 11 12 10 11 12 13 + 10 11 12 13 11 12 13 14 + 11 12 13 14 12 13 14 15 + 12 13 14 15 13 14 15 16 + 14 15 16 17 15 16 17 18 + 15 16 17 18 16 17 18 19 + 16 17 18 19 17 18 19 20 + 17 18 19 20 18 19 20 21 + 18 19 20 21 19 20 21 22 + 19 20 21 22 20 21 22 23 + 20 21 22 23 21 22 23 24 + 21 22 23 24 22 23 24 25 + 22 23 24 25 23 24 25 26 + 23 24 25 26 24 25 26 27 + 24 25 26 27 + + 0 !NIMPHI: impropers + + + 0 !NDON: donors + + + 0 !NACC: acceptors + + + 0 !NNB + + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 + + 1 0 !NGRP + 0 0 0 + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=0tau_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=0tau_LR.jpg new file mode 100644 index 0000000000..152fa88ff9 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=0tau_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=200tau_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=200tau_LR.jpg new file mode 100644 index 0000000000..bb269f47f2 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=200tau_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated.lt new file mode 100644 index 0000000000..0dc1f5dd05 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated.lt @@ -0,0 +1,255 @@ +# This file defines a pair of coarse-grained protein models used in: +# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) +# (http://www.pnas.org/content/101/36/13192) + + +1beadUnfrustrated { + + # Note: the "unfrustrated" model is kind of funny looking. (My apologies.) + + # There are 3 atom types (referred to above as B, L, and N) + # Define their masses: + + write_once("Data Masses") { + @atom:B 1.0 + @atom:L 1.0 + @atom:N 1.0 + } + + # AtomID MoleculeID AtomType Charge X Y Z + + write("Data Atoms") { + $atom:a1 $mol @atom:L 0.0 -1.3969548 1.7525716 -0.28565118 + $atom:a2 $mol @atom:B 0.0 -0.66847917 1.0738923 -0.39651074 + $atom:a3 $mol @atom:L 0.0 -0.16610379 1.0893417 0.44519456 + $atom:a4 $mol @atom:B 0.0 0.42244126 0.35006314 0.15979926 + $atom:a5 $mol @atom:L 0.0 1.2844393 0.55103218 0.64505356 + $atom:a6 $mol @atom:N 0.0 1.9703715 0.37775946 -0.05267634 + $atom:a7 $mol @atom:N 0.0 2.574926 -0.30399114 0.34330503 + $atom:a8 $mol @atom:N 0.0 2.029546 -1.1256647 0.19829852 + $atom:a9 $mol @atom:B 0.0 1.0936146 -0.76054936 0.1043528 + $atom:a10 $mol @atom:L 0.0 0.74888247 -0.81165991 1.0334863 + $atom:a11 $mol @atom:B 0.0 -0.069536333 -0.26815389 0.94356636 + $atom:a12 $mol @atom:L 0.0 -0.65671052 -0.522532 1.7113065 + $atom:a13 $mol @atom:N 0.0 -1.5278507 -0.10774689 1.4611921 + $atom:a14 $mol @atom:L 0.0 -2.1958878 -0.8403146 1.5521738 + $atom:a15 $mol @atom:N 0.0 -2.6058074 -0.86553455 0.64397232 + $atom:a16 $mol @atom:N 0.0 -1.8447588 -1.1286421 0.042924693 + $atom:a17 $mol @atom:N 0.0 -1.5328721 -0.28576244 -0.40564841 + $atom:a18 $mol @atom:B 0.0 -0.69593879 0.027664412 0.064884008 + $atom:a19 $mol @atom:B 0.0 0.0026517494 -0.66355162 -0.11470678 + $atom:a20 $mol @atom:L 0.0 -0.35479285 -1.2282381 -0.86455878 + $atom:a21 $mol @atom:L 0.0 -0.60202976 -0.47829758 -1.4411001 + $atom:a22 $mol @atom:B 0.0 -0.14616501 0.20157397 -0.87098365 + $atom:a23 $mol @atom:B 0.0 0.7755198 -0.14153019 -0.76838748 + $atom:a24 $mol @atom:L 0.0 1.2465693 0.19738595 -1.5794731 + $atom:a25 $mol @atom:L 0.0 0.77604792 1.0612244 -1.637442 + $atom:a26 $mol @atom:B 0.0 0.44801303 1.1110219 -0.6900789 + $atom:a27 $mol @atom:L 0.0 1.0908651 1.7386382 -0.24229241 + } + + # bond-ID bond-Type atom-ID atom-ID + + write("Data Bonds") { + $bond:b1 @bond:backbone $atom:a1 $atom:a2 + $bond:b2 @bond:backbone $atom:a2 $atom:a3 + $bond:b3 @bond:backbone $atom:a3 $atom:a4 + $bond:b4 @bond:backbone $atom:a4 $atom:a5 + $bond:b5 @bond:backbone $atom:a5 $atom:a6 + $bond:b6 @bond:backbone $atom:a6 $atom:a7 + $bond:b7 @bond:backbone $atom:a7 $atom:a8 + $bond:b8 @bond:backbone $atom:a8 $atom:a9 + $bond:b9 @bond:backbone $atom:a9 $atom:a10 + $bond:b10 @bond:backbone $atom:a10 $atom:a11 + $bond:b11 @bond:backbone $atom:a11 $atom:a12 + $bond:b12 @bond:backbone $atom:a12 $atom:a13 + $bond:b13 @bond:backbone $atom:a13 $atom:a14 + $bond:b14 @bond:backbone $atom:a14 $atom:a15 + $bond:b15 @bond:backbone $atom:a15 $atom:a16 + $bond:b16 @bond:backbone $atom:a16 $atom:a17 + $bond:b17 @bond:backbone $atom:a17 $atom:a18 + $bond:b18 @bond:backbone $atom:a18 $atom:a19 + $bond:b19 @bond:backbone $atom:a19 $atom:a20 + $bond:b20 @bond:backbone $atom:a20 $atom:a21 + $bond:b21 @bond:backbone $atom:a21 $atom:a22 + $bond:b22 @bond:backbone $atom:a22 $atom:a23 + $bond:b23 @bond:backbone $atom:a23 $atom:a24 + $bond:b24 @bond:backbone $atom:a24 $atom:a25 + $bond:b25 @bond:backbone $atom:a25 $atom:a26 + $bond:b26 @bond:backbone $atom:a26 $atom:a27 + } + + # (3-body) Angles are specified below + + # (4-body) Dihedrals must be defined explicitly for every quartet of atoms. + # (These interactions are not determined by atom type.) + # + # Note that some quartets of atoms are listed because their + # potentials contain multiple terms in the Fourier expansion. + # (IE. multiple cosines... Be sure to use "-overlay-dihedrals"!) + # + # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID + + write("Data Dihedrals") { + $dihedral:d1a @dihedral:beta1 $atom:a1 $atom:a2 $atom:a3 $atom:a4 + $dihedral:d1b @dihedral:beta2 $atom:a1 $atom:a2 $atom:a3 $atom:a4 + $dihedral:d2a @dihedral:beta1 $atom:a2 $atom:a3 $atom:a4 $atom:a5 + $dihedral:d2b @dihedral:beta2 $atom:a2 $atom:a3 $atom:a4 $atom:a5 + $dihedral:d3a @dihedral:beta1 $atom:a3 $atom:a4 $atom:a5 $atom:a6 + $dihedral:d3b @dihedral:beta2 $atom:a3 $atom:a4 $atom:a5 $atom:a6 + $dihedral:d4a @dihedral:beta1 $atom:a4 $atom:a5 $atom:a6 $atom:a7 + $dihedral:d4b @dihedral:beta2 $atom:a4 $atom:a5 $atom:a6 $atom:a7 + $dihedral:d5 @dihedral:turn1 $atom:a5 $atom:a6 $atom:a7 $atom:a8 + $dihedral:d6 @dihedral:turn2 $atom:a6 $atom:a7 $atom:a8 $atom:a9 + $dihedral:d7 @dihedral:turn3 $atom:a7 $atom:a8 $atom:a9 $atom:a10 + $dihedral:d8a @dihedral:beta1 $atom:a8 $atom:a9 $atom:a10 $atom:a11 + $dihedral:d8b @dihedral:beta2 $atom:a8 $atom:a9 $atom:a10 $atom:a11 + $dihedral:d9a @dihedral:beta1 $atom:a9 $atom:a10 $atom:a11 $atom:a12 + $dihedral:d9b @dihedral:beta2 $atom:a9 $atom:a10 $atom:a11 $atom:a12 + $dihedral:d10a @dihedral:beta1 $atom:a10 $atom:a11 $atom:a12 $atom:a13 + $dihedral:d10b @dihedral:beta2 $atom:a10 $atom:a11 $atom:a12 $atom:a13 + $dihedral:d11a @dihedral:beta1 $atom:a11 $atom:a12 $atom:a13 $atom:a14 + $dihedral:d11b @dihedral:beta2 $atom:a11 $atom:a12 $atom:a13 $atom:a14 + $dihedral:d12a @dihedral:beta1 $atom:a12 $atom:a13 $atom:a14 $atom:a15 + $dihedral:d12b @dihedral:beta2 $atom:a12 $atom:a13 $atom:a14 $atom:a15 + $dihedral:d13 @dihedral:turn4 $atom:a13 $atom:a14 $atom:a15 $atom:a16 + $dihedral:d14 @dihedral:turn5 $atom:a14 $atom:a15 $atom:a16 $atom:a17 + $dihedral:d15a @dihedral:alpha1 $atom:a15 $atom:a16 $atom:a17 $atom:a18 + $dihedral:d15b @dihedral:alpha2 $atom:a15 $atom:a16 $atom:a17 $atom:a18 + $dihedral:d16a @dihedral:alpha1 $atom:a16 $atom:a17 $atom:a18 $atom:a19 + $dihedral:d16b @dihedral:alpha2 $atom:a16 $atom:a17 $atom:a18 $atom:a19 + $dihedral:d17a @dihedral:alpha1 $atom:a17 $atom:a18 $atom:a19 $atom:a20 + $dihedral:d17b @dihedral:alpha2 $atom:a17 $atom:a18 $atom:a19 $atom:a20 + $dihedral:d18a @dihedral:alpha1 $atom:a18 $atom:a19 $atom:a20 $atom:a21 + $dihedral:d18b @dihedral:alpha2 $atom:a18 $atom:a19 $atom:a20 $atom:a21 + $dihedral:d19a @dihedral:alpha1 $atom:a19 $atom:a20 $atom:a21 $atom:a22 + $dihedral:d19b @dihedral:alpha2 $atom:a19 $atom:a20 $atom:a21 $atom:a22 + $dihedral:d20a @dihedral:alpha1 $atom:a20 $atom:a21 $atom:a22 $atom:a23 + $dihedral:d20b @dihedral:alpha2 $atom:a20 $atom:a21 $atom:a22 $atom:a23 + $dihedral:d21a @dihedral:alpha1 $atom:a21 $atom:a22 $atom:a23 $atom:a24 + $dihedral:d21b @dihedral:alpha2 $atom:a21 $atom:a22 $atom:a23 $atom:a24 + $dihedral:d22a @dihedral:alpha1 $atom:a22 $atom:a23 $atom:a24 $atom:a25 + $dihedral:d22b @dihedral:alpha2 $atom:a22 $atom:a23 $atom:a24 $atom:a25 + $dihedral:d23a @dihedral:alpha1 $atom:a23 $atom:a24 $atom:a25 $atom:a26 + $dihedral:d23b @dihedral:alpha2 $atom:a23 $atom:a24 $atom:a25 $atom:a26 + $dihedral:d24a @dihedral:alpha1 $atom:a24 $atom:a25 $atom:a26 $atom:a27 + $dihedral:d24b @dihedral:alpha2 $atom:a24 $atom:a25 $atom:a26 $atom:a27 + } + + # All consecutively bonded triplets of atoms same 3-body bond-angle + # interaction parameters. Of coarse, we could specify them all explicitly + # (as we did for the dihedrals above), but I wanted to show how to specify + # angles by atom type instead. (You can do this for dihedrals & impropers + # also.) + + # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type + + write_once("Data Angles By Type") { + @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* + } + + # (The "*" is a wildcard character. I use "*" to denote any atom-type or + # bond-type which is defined within the current namespace: 1beadUnfrustrated) + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 + pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0 + pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0 + pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1 + pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0 + pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0 + } + + + # 2-body (bonded) interactions: + # + # Ubond(r) = (k/2)*(r-0)^2 + # + # The corresponding command is: + # + # bond-Type bondstylename k r0 + + write_once("In Settings") { + bond_coeff @bond:backbone harmonic 100.0 1.0 + } + + # 3-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Uangle(theta) = (k/2)*(theta-theta0)^2 + # (k in kcal/mol/rad^2, theta0 in degrees) + # + # angle-Type anglestylename k theta0 + + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 13.3333333333 105.0 + } + + # 4-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Udihedral(phi) = K * (1 + cos(n*phi - d)) + # + # The d parameter is in degrees, K is in kcal/mol/rad^2. + # + # The corresponding command is: + # + # dihedral_coeff dihedralType dihedralstylename K n d w + # ("w" is the weight for 1-4 pair interactions, which we set to 0) + + # NOTE: Currently, dihedral_coeff charmm does not allow non-integer d + # parameters. I'm hoping this will be fixed eventually. + + write_once("In Settings") { + # Correct version: + #dihedral_coeff @dihedral:alpha1 charmm -1.5 1 57.2957795 0.0 + # Replacing with + dihedral_coeff @dihedral:alpha1 charmm -1.5 1 57 0.0 + # Correct version: + #dihedral_coeff @dihedral:alpha2 charmm 0.375 2 114.591559 0.0 + # Replacing with + dihedral_coeff @dihedral:alpha2 charmm 0.375 2 115 0.0 + dihedral_coeff @dihedral:beta1 charmm -1.5 1 180 0.0 + dihedral_coeff @dihedral:beta2 charmm 0.375 2 360 0.0 + dihedral_coeff @dihedral:turn1 charmm -3.0 1 90 0.0 + # Correct version: + # dihedral_coeff @dihedral:turn2 charmm -3.0 1 11.4591559 0.0 + # Replacing with + dihedral_coeff @dihedral:turn2 charmm -3.0 1 11 0.0 + dihedral_coeff @dihedral:turn3 charmm -3.0 1 -90 0.0 + dihedral_coeff @dihedral:turn4 charmm 0.0 1 0 0.0 + dihedral_coeff @dihedral:turn5 charmm 0.0 1 0 0.0 + } + + write_once("In Settings") { + # Optional: define the atoms in the "proteins" group + group proteins type @atom:B + group proteins type @atom:L + group proteins type @atom:N + } + + # LAMMPS has many available force field styles (and atom styles). + # Here, we pick the ones which work well for this molecular model: + + write_once("In Init") { + # --- Default options for the "1BeadUnfrustrated" protein model --- + # --- (These can be overridden later.) --- + units lj + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid charmm + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + +} # 1beadUnfrustrated + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated_variants.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated_variants.lt new file mode 100644 index 0000000000..cbc8fe217c --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated_variants.lt @@ -0,0 +1,45 @@ +import "1beadUnfrustrated.lt" + + +# Alternate starting conformation (same molecule): + + +1beadUnfolded inherits 1beadUnfrustrated { + + # This molecule "inherits" all of its features from "1beadUnfrustrated" + # Here we override the atomic positions with new coordinates: + + # AtomID MoleculeID AtomType Charge X Y Z + + write("Data Atoms") { + $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0 + $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8 + $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8 + $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0 + $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0 + $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8 + $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8 + $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0 + $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0 + $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8 + $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8 + $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0 + $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0 + $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8 + $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8 + $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2 + $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2 + $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6 + $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6 + $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2 + $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2 + $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6 + $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6 + $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2 + $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2 + $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6 + $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6 + } + +} # 1beadUnfolded + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/system.lt new file mode 100644 index 0000000000..5ebe6efb88 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/system.lt @@ -0,0 +1,11 @@ +import "1beadUnfrustrated_variants.lt" + + +protein = new 1beadUnfolded # (unfolded conformation, unfrustrated protein) + + +write_once("Data Boundary") { + 0.0 27.0 xlo xhi + 0.0 27.0 ylo yhi + 0.0 27.0 zlo zhi +} diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.min b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.min new file mode 100644 index 0000000000..fce9843aa8 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.min @@ -0,0 +1,19 @@ +# -- Init section -- + +include system.in.init + +# -- Atom definition section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run section -- + +dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz + +minimize 1.0e-5 1.0e-7 500 2000 + +write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.nvt new file mode 100644 index 0000000000..a831a97b4a --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.nvt @@ -0,0 +1,46 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +# I you want to be careful, you can minimize the system first. (Try using +# "run.in.min" and uncomment the read_restart command in this file below.) +# read_restart system_after_min.rst + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 0.025 +dump 1 all custom 50 traj_nvt.lammpstrj id mol type x y z ix iy iz + +# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". +# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) + +fix fxlan all langevin 0.39 0.39 1.0 48279 +fix fxnve all nve + +# Notes: +# The temperature is in reduced units and is set to 0.39 +# which is the folding temperature for the unfrustrated protein. +# The inverse-damping-rate "damp" (which has units of time) is set to 1.0, +# as it was in the paper. (Hopefully folding times should be similar.) +# (See http://lammps.sandia.gov/doc/fix_langevin.html) + + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo_modify norm no #(report total energy not energy / num_atoms) +thermo 50 #(time interval for printing out "thermo" data) + +#restart 100000000 restart_nvt + +run 8000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README.TXT new file mode 100644 index 0000000000..eda6a1ca22 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README.TXT @@ -0,0 +1,44 @@ +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. + +This is an example of a very simple coarse-grained protein. + +This example contains a 1-bead (C-alpha model) representation of the +"unfrustrated" 4-helix bundle model used in this paper: +G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) + +In this model, there are three atom-types (bead-types), H, L, and N +representing one amino-acid each. The "H" beads represent the hydrophobic +amino acids, and are attracted to eachother with a strength of "1.0" +(in dimensionless units of "epsilon"). The "L" and "N" atoms are +hydrophilic and purely repulsive, and only differ in their secondary-structure +propensity (ie their dihedral parameters). + +The dihedral-interaction is bi-stable with two deep local minima (corresponding +to helix-like and sheet-like secondary structure). You can adjust the bias +in favor of one minima or another by modifying the angle-shift parameter in +the appropriate "dihedral_coeff" command in the other .lt file. + +A definition for the 4-sheet beta-barell protein model is also included. +If you want to simulate that molecule instead, then edit the "system.lt" +file (in the "moltemplate_files" subdirectory), and replace this line: +prot = new 4HelixBundle + with +prot = new 4SheetBundle + +------------- +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_run.sh new file mode 100755 index 0000000000..45bd2d451d --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_run.sh @@ -0,0 +1,31 @@ +# You would probably run lammps this way: +# +# lmp_ubuntu -i run.in.nvt + +# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer +# to the input scripts & data files you created earlier when you ran moltemplate +# system.in.init, system.in.settings, system.data + + + + +# ----------------------------------- + + + +LAMMPS_COMMAND="lmp_ubuntu" + +# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps +# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. + +# Run lammps using the following 3 commands: + +"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +"$LAMMPS_COMMAND" -i run.in.nvt # production run + +# Alternately, if you have MPI installed, try something like this: + +#NUMPROCS=4 +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) +#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_setup.sh new file mode 100755 index 0000000000..cb3196cf8a --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_setup.sh @@ -0,0 +1,23 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -overlay-dihdedrals system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/4HelixBundle_t=0.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/4HelixBundle_t=0.jpg new file mode 100644 index 0000000000..b4d919f9e6 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/4HelixBundle_t=0.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/4SheetBundle_t=0.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/4SheetBundle_t=0.jpg new file mode 100644 index 0000000000..cd65146ffa Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/4SheetBundle_t=0.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 0000000000..de47509ed4 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,214 @@ +PSF + + 1 !NTITLE + REMARKS VMD generated structure x-plor psf file + + 73 !NATOM + 1 1 1 1 0.000000 1.0000 0 + 2 1 1 1 0.000000 1.0000 0 + 3 1 2 2 0.000000 1.0000 0 + 4 1 2 2 0.000000 1.0000 0 + 5 1 1 1 0.000000 1.0000 0 + 6 1 1 1 0.000000 1.0000 0 + 7 1 2 2 0.000000 1.0000 0 + 8 1 2 2 0.000000 1.0000 0 + 9 1 1 1 0.000000 1.0000 0 + 10 1 1 1 0.000000 1.0000 0 + 11 1 2 2 0.000000 1.0000 0 + 12 1 2 2 0.000000 1.0000 0 + 13 1 1 1 0.000000 1.0000 0 + 14 1 1 1 0.000000 1.0000 0 + 15 1 2 2 0.000000 1.0000 0 + 16 1 2 2 0.000000 1.0000 0 + 17 1 1 1 0.000000 1.0000 0 + 18 1 1 1 0.000000 1.0000 0 + 19 1 2 2 0.000000 1.0000 0 + 20 1 2 2 0.000000 1.0000 0 + 21 1 1 1 0.000000 1.0000 0 + 22 1 1 1 0.000000 1.0000 0 + 23 1 2 2 0.000000 1.0000 0 + 24 1 2 2 0.000000 1.0000 0 + 25 1 1 1 0.000000 1.0000 0 + 26 1 1 1 0.000000 1.0000 0 + 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47 48 71 72 63 64 73 72 + 14 15 16 65 30 31 32 67 + 46 47 48 71 62 63 64 73 + + 0 !NIMPHI: impropers + + + 0 !NDON: donors + + + 0 !NACC: acceptors + + + 0 !NNB + + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 + + 1 0 !NGRP + 0 0 0 + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/1beadProtSci2010.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/1beadProtSci2010.lt new file mode 100644 index 0000000000..9b4ff25354 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/1beadProtSci2010.lt @@ -0,0 +1,274 @@ +# This file defines a family of coarse-grained protein models used in: +# G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) +# +# Strategy: +# +#1) First I'll define some building blocks (A16, B16, T3) +# which are helices, sheets and turns of a predetermined length) +# +#2) Then I'll copy and paste them together to build +# a 4-helix bundle or a 4-strand beta-barrel. +# This approach is optional. If your protein has helices which are not +# identical, you should probably just include all 4 helices in a single +# "Data Atoms" section and don't try to subdivide the protein into pieces.) + + +1beadProtSci2010 { # <-- enclose definitions in a namespace for portability + + write_once("In Init") { + units lj + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid fourier + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + + + # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each) + + A16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../L 0.0 -0.4 -0.4 0.0 + $atom:a2 $mol:... @atom:../L 0.0 0.4 -0.4 0.6 + $atom:a3 $mol:... @atom:../H 0.0 0.4 0.4 1.2 + $atom:a4 $mol:... @atom:../H 0.0 -0.4 0.4 1.8 + $atom:a5 $mol:... @atom:../L 0.0 -0.4 -0.4 2.4 + $atom:a6 $mol:... @atom:../L 0.0 0.4 -0.4 3.0 + $atom:a7 $mol:... @atom:../H 0.0 0.4 0.4 3.6 + $atom:a8 $mol:... @atom:../H 0.0 -0.4 0.4 4.2 + $atom:a9 $mol:... @atom:../L 0.0 -0.4 -0.4 4.8 + $atom:a10 $mol:... @atom:../L 0.0 0.4 -0.4 5.4 + $atom:a11 $mol:... @atom:../H 0.0 0.4 0.4 6.0 + $atom:a12 $mol:... @atom:../H 0.0 -0.4 0.4 6.6 + $atom:a13 $mol:... @atom:../L 0.0 -0.4 -0.4 7.2 + $atom:a14 $mol:... @atom:../L 0.0 0.4 -0.4 7.8 + $atom:a15 $mol:... @atom:../H 0.0 0.4 0.4 8.4 + $atom:a16 $mol:... @atom:../H 0.0 -0.4 0.4 9.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # A16 + + + # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each) + + B16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../L 0.0 -0.3 0.0 0.0 + $atom:a2 $mol:... @atom:../H 0.0 0.3 0.0 0.8 + $atom:a3 $mol:... @atom:../L 0.0 -0.3 0.0 1.6 + $atom:a4 $mol:... @atom:../H 0.0 0.3 0.0 2.4 + $atom:a5 $mol:... @atom:../L 0.0 -0.3 0.0 3.2 + $atom:a6 $mol:... @atom:../H 0.0 0.3 0.0 4.0 + $atom:a7 $mol:... @atom:../L 0.0 -0.3 0.0 4.8 + $atom:a8 $mol:... @atom:../H 0.0 0.3 0.0 5.6 + $atom:a9 $mol:... @atom:../L 0.0 -0.3 0.0 6.4 + $atom:a10 $mol:... @atom:../H 0.0 0.3 0.0 7.2 + $atom:a11 $mol:... @atom:../L 0.0 -0.3 0.0 8.0 + $atom:a12 $mol:... @atom:../H 0.0 0.3 0.0 8.8 + $atom:a13 $mol:... @atom:../L 0.0 -0.3 0.0 9.6 + $atom:a14 $mol:... @atom:../H 0.0 0.3 0.0 10.4 + $atom:a15 $mol:... @atom:../L 0.0 -0.3 0.0 11.2 + $atom:a16 $mol:... @atom:../H 0.0 0.3 0.0 12.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # B16 + + T3 { # T3 is a "turn" region consisting of 3 beads + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../N 0.0 -0.8 0.0 0.0 + $atom:a2 $mol:... @atom:../N 0.0 0.0 0.55 -0.24 + $atom:a3 $mol:... @atom:../N 0.0 0.8 0.0 0.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + } + + } # T3 + + # ----- Now build larger molecules using A16, B16 and T3 ------- + + 4SheetBarrel { + + sheet1 = new B16.rot( 45, 0,0,1).move(-0.793700526,-0.793700526, -6) + sheet2 = new B16.rot( 135, 0,0,1).move( 0.793700526,-0.793700526, -6) + sheet3 = new B16.rot( 225, 0,0,1).move( 0.793700526, 0.793700526, -6) + sheet4 = new B16.rot( 315, 0,0,1).move(-0.793700526, 0.793700526, -6) + + turn1 = new T3.rot(180,1,0,0).rot(0,0,0,1).move(0,-1.3,6.6) + turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(0.7,-0.0,-6.9) + turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move(0,1.3,6.6) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + } + + + 4HelixBundle { + + helix1 = new A16.rot( -45, 0,0,1).move(-1.12691645,-1.12691645, -4.5) + helix2 = new A16.rot( 45, 0,0,1).move( 1.12691645,-1.12691645, -4.5) + helix3 = new A16.rot( 135, 0,0,1).move( 1.12691645, 1.12691645, -4.5) + helix4 = new A16.rot( 225, 0,0,1).move(-1.12691645, 1.12691645, -4.5) + + turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-0.2,-0.7,5.4) + turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(0.7,-0.15,-4.8) + turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(0.2,0.7,5.4) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + } + + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:H @atom:H lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 + pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 1.0 1.0 1 0 + pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 1.0 1.0 1 0 + } + # Interactions between different atoms use "repulsive wins" mixing rules + + + # bond_coeff bondType bondstylename k r0 + + write_once("In Settings") { + bond_coeff @bond:backbone harmonic 66.6 1.0 + } + + + # angle_coeff angleType anglestylename k theta0 + + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 66.6 105.0 + } + + # We use the same bond-angle forces whenever + # there are 3 consecutively-bonded atoms: + # + # angleType atomtypes1 2 3 bondtypes1 2 + + write_once("Data Angles By Type") { + @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* + } + + + + # From the Bellesia et al 2010 paper: + # for helices: U_{dih}(\phi) = 1.2*(cos(3\phi) + cos(\phi+\delta)) + # for turns: U_{dih}(\phi) = 0.2*cos(3\phi) + # + # General formula used for "dihedral_style fourier": + # U_{dih}(\phi) = \Sum_{i=1}^m K_i [ 1.0 + cos(n_i \phi - d_i) ] + # + # Syntax: + # dihedralType dihedralstyle m K_1 n_1 d_1 K2 n_2 d_2 ... + + write_once("In Settings") { + dihedral_coeff @dihedral:delta60_0 fourier 2 2.167862 3 0 2.167862 1 -60.0 + dihedral_coeff @dihedral:delta62_5 fourier 2 2.167862 3 0 2.167862 1 -62.5 + dihedral_coeff @dihedral:delta65_0 fourier 2 2.167862 3 0 2.167862 1 -65.0 + dihedral_coeff @dihedral:turn fourier 1 0.361310 3 0 + # Note: 2.167862=1.2*epsilon and 0.361310=0.2*epsilon. + } + + + # dihedralType atomtypes1 2 3 4 bondtypes1 2 3 + + write_once("Data Dihedrals By Type") { + @dihedral:delta60_0 @atom:H @atom:L @atom:H @atom:L * * * + @dihedral:delta60_0 @atom:H @atom:H @atom:L @atom:L * * * + @dihedral:delta60_0 @atom:H @atom:L @atom:L @atom:H * * * + @dihedral:delta60_0 @atom:L @atom:H @atom:H @atom:L * * * + @dihedral:turn @atom:N @atom:* @atom:* @atom:* * * * + } + # Note: This next rule is not needed: + # @dihedral:turn @atom:* @atom:* @atom:* @atom:N * * * + # (By reflection symmetry, it's equivalent to the rule above.) + # + # Note: The example in ../../membrane+protein/moltemplate_files/ + # demonstrates how to define dihedral angles for this model + # in an alternate way which might be easier to understand. + + + # --- Mass Units --- + # There are 3 atom types (referred to above as ../H, ../L, and ../N) + # Define their masses (in reduced units): + + write_once("Data Masses") { + @atom:H 1.0 + @atom:L 1.0 + @atom:N 1.0 + } + + +} # 1beadProtSci2010 (namespace) + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/README.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/README.sh new file mode 100755 index 0000000000..852b9b76f2 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/README.sh @@ -0,0 +1,13 @@ +# run moltemplate this way + +moltemplate.sh system.lt + +# This will generate various files with names ending in *.in* and *.data +# which are needed by LAMMPS. + +# ------ Other versions: -------- +# +# If you are using the "other_versions/charmm/1beadProtSci2010.lt" file, +# then you must run moltemplate this way: +# +# moltemplate.sh -overlay-dihdedrals system.lt diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/README.TXT new file mode 100644 index 0000000000..82bc8c5c43 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/README.TXT @@ -0,0 +1,13 @@ +This directory contains other versions of the same molecule +(with the same force-field), implemented in different ways. + +charmm/1beadProtSci2010.lt <-- This applies multiple "charmm" dihedral angle + forces to the same quartet of atoms to create + a Fourier series. (No packages needed.) + + NOTE: You must run moltemplate this way: + + moltemplate.sh -overlay-dihdedrals system.lt + +class2/1beadProtSci2010.lt <-- This uses the "class2" dihedral angles forces + (You must build LAMMPS with the CLASS2 package) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/charmm/1beadProtSci2010.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/charmm/1beadProtSci2010.lt new file mode 100644 index 0000000000..d57186bee7 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/charmm/1beadProtSci2010.lt @@ -0,0 +1,411 @@ +# This file defines a family of coarse-grained protein models used in: +# G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) +# +# +# For portability, all definitions in this file are enclosed within +# the "1beadProtSci2010" namespace. To access them, put +# "using namespace 1beadProtSci2010" in your LT file. + +# Strategy: +# +#1) First I'll define some building blocks +# (short helices, sheets and turns of a predetermined length) +# +#2) Then I'll cut and paste them together to build +# a 4-helix bundle or a 4-strand beta-barrel. +# +# Doing it this way is optional. It's simpler (but longer) to simply write +# out the entire sequence of all 73 atoms in a single "Data Atoms" section. +# (IE. Don't try to subdivide it.) It's also simpler to explicitly list the +# 72 bonds, 71 3-body angles and 70 4-body dihedral angle interactions +# manually (instead of inferring them from the atom type). If your protein +# has helices which are not identical, this would probably be easier. +# Use whichever style you prefer. +# +# +# Note that atom types, bond types, angle types, and dihedral types +# are shared between all molecules defined in the "1beadProtSci2010" family. +# (That's why there is a "../" in their path-names. Otherwise atom, bond, +# angle types, etc... are not shared between different molecules.) +# +# Confusing detail: +# Each molecule in LAMMPS can be assigned a unique molecule-ID (an integer). +# These are represented by the "$mol" variable written next to each atom. +# Our protein has multiple subunits (in this case: helices, sheets, turns). +# Because we want the subunits to share the same molecule-ID counter we use +# "$mol:..." instead of "$mol" which tells moltemplate to search for the +# parent molecule's ID. This is optional. If it bothers you, just use "$mol" + + + +1beadProtSci2010 { + + write_once("In Init") { + # -- Default styles for "1beadProtSci2010" -- + units lj + atom_style full + # (Hybrid force fields were not necessary but are used for portability.) + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid charmm + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 + + # If charges are needed, (assuming biopolymers), try one of: + #dielectric 80.0 + #pair_style hybrid lj/cut/coul/debye 0.1 4.0 + # or (for short distances, below a couple nm) + #pair_style hybrid lj/charmm/coul/charmm/implicit 3.5 4.0 + + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + + + # ---- Building blocks: A16, B16, Turn3 ---- + + # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each) + + A16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../L 0.0 -0.4 -0.4 0.0 + $atom:a2 $mol:... @atom:../L 0.0 0.4 -0.4 0.6 + $atom:a3 $mol:... @atom:../H 0.0 0.4 0.4 1.2 + $atom:a4 $mol:... @atom:../H 0.0 -0.4 0.4 1.8 + $atom:a5 $mol:... @atom:../L 0.0 -0.4 -0.4 2.4 + $atom:a6 $mol:... @atom:../L 0.0 0.4 -0.4 3.0 + $atom:a7 $mol:... @atom:../H 0.0 0.4 0.4 3.6 + $atom:a8 $mol:... @atom:../H 0.0 -0.4 0.4 4.2 + $atom:a9 $mol:... @atom:../L 0.0 -0.4 -0.4 4.8 + $atom:a10 $mol:... @atom:../L 0.0 0.4 -0.4 5.4 + $atom:a11 $mol:... @atom:../H 0.0 0.4 0.4 6.0 + $atom:a12 $mol:... @atom:../H 0.0 -0.4 0.4 6.6 + $atom:a13 $mol:... @atom:../L 0.0 -0.4 -0.4 7.2 + $atom:a14 $mol:... @atom:../L 0.0 0.4 -0.4 7.8 + $atom:a15 $mol:... @atom:../H 0.0 0.4 0.4 8.4 + $atom:a16 $mol:... @atom:../H 0.0 -0.4 0.4 9.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # A16 + + + # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each) + + B16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../L 0.0 -0.3 0.0 0.0 + $atom:a2 $mol:... @atom:../H 0.0 0.3 0.0 0.8 + $atom:a3 $mol:... @atom:../L 0.0 -0.3 0.0 1.6 + $atom:a4 $mol:... @atom:../H 0.0 0.3 0.0 2.4 + $atom:a5 $mol:... @atom:../L 0.0 -0.3 0.0 3.2 + $atom:a6 $mol:... @atom:../H 0.0 0.3 0.0 4.0 + $atom:a7 $mol:... @atom:../L 0.0 -0.3 0.0 4.8 + $atom:a8 $mol:... @atom:../H 0.0 0.3 0.0 5.6 + $atom:a9 $mol:... @atom:../L 0.0 -0.3 0.0 6.4 + $atom:a10 $mol:... @atom:../H 0.0 0.3 0.0 7.2 + $atom:a11 $mol:... @atom:../L 0.0 -0.3 0.0 8.0 + $atom:a12 $mol:... @atom:../H 0.0 0.3 0.0 8.8 + $atom:a13 $mol:... @atom:../L 0.0 -0.3 0.0 9.6 + $atom:a14 $mol:... @atom:../H 0.0 0.3 0.0 10.4 + $atom:a15 $mol:... @atom:../L 0.0 -0.3 0.0 11.2 + $atom:a16 $mol:... @atom:../H 0.0 0.3 0.0 12.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # B16 + + T3 { # T3 is a "turn" region consisting of 3 beads + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../N 0.0 -0.8 0.0 0.0 + $atom:a2 $mol:... @atom:../N 0.0 0.0 0.55 -0.24 + $atom:a3 $mol:... @atom:../N 0.0 0.8 0.0 0.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + } + + } # T3 + + # (Note: Again, atom types, bond-types, (dihedral-types, any variable, etc) + # can be shared. The ".." in "@atom:../CA" tells moltemplate that + # atom type CA is defined in the parent's environment. (We are + # sharing the CA atom type between both the H and P residues. + # The same is true of the ".." in "@bond:../sidechain". + # + # + # Note: The "..." in "$mol:..." tells moltemplate that this molecule may + # be a part of a larger molecule, and (if so) to use the larger + # molecule's id number as it's own. + + + + # ----- Now build larger molecules using A16, B16 and T3 ------- + + 4HelixBundle { + + helix1 = new A16.rot( -45, 0,0,1).move(-1.12691645,-1.12691645, 0) + helix2 = new A16.rot( 45, 0,0,1).move( 1.12691645,-1.12691645, 0) + helix3 = new A16.rot( 135, 0,0,1).move( 1.12691645, 1.12691645, 0) + helix4 = new A16.rot( 225, 0,0,1).move(-1.12691645, 1.12691645, 0) + # Note: 1.12691645 ~= 0.5*2^(1/6) + 0.4*sqrt(2) + + turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-0.2,-0.7,9.9) + turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(0.7,-0.15,-0.3) + turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(0.2,0.7,9.9) + + # Note: In the paper, this is described as the "UA2" conformation + # (I played around with the angles until it looked "okay". This is not + # the minimum energy conformation. Further minimization is necessary.) + + # Now bond the pieces together. + # (Note: angle & dihedral interactions will be generated automatically.) + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # <-- create a variable for the parent's Molecule-ID + } + + 4SheetBundle { + + sheet1 = new B16.rot( 45, 0,0,1).move(-0.793700526,-0.793700526, 0) + sheet2 = new B16.rot( 135, 0,0,1).move( 0.793700526,-0.793700526, 0) + sheet3 = new B16.rot( 225, 0,0,1).move( 0.793700526, 0.793700526, 0) + sheet4 = new B16.rot( 315, 0,0,1).move(-0.793700526, 0.793700526, 0) + # Note: 0.793700526 ~= 0.5*2^(1/6) * sqrt(1/2) + + turn1 = new T3.rot(180,1,0,0).rot(0,0,0,1).move(0,-1.3,12.6) + turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(0.7,-0.0,-0.9) + turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move(0,1.3,12.6) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + } + + + # There are 3 atom types (referred to above as ../H, ../L, and ../N) + # Define their masses: + + write_once("Data Masses") { + @atom:H 1.0 + @atom:L 1.0 + @atom:N 1.0 + + } + + + + # -------------------------------------------------------------------- + # -- In this example, all force field parameters are stored in the -- + # -- file named "In Settings". They can also go in sections like -- + # -- "Data Pair Coeffs", "Data Bond Coeffs", "Data Angle Coeffs"... -- + # -------------------------------------------------------------------- + + + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:H @atom:H lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 + pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 1.0 1.0 1 0 + pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 1.0 1.0 1 0 + } + # (Interactions between different atom types use "arithmetic" + # and "maxmax" ("repulsion-wins") mixing rules.) + + + # 2-body (bonded) interactions: + # + # Ubond(r) = (k/2)*(r-0)^2 + # + # The corresponding command is: + # + # bond_coeff bondType bondstylename k r0 + # + + write_once("In Settings") { + bond_coeff @bond:backbone harmonic 66.6 1.0 + } + + + + # 3-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Uangle(theta) = (k/2)*(theta-theta0)^2 + # (k in kcal/mol/rad^2, theta0 in degrees) + # + # The corresponding command is: + # + # angle_coeff angleType anglestylename k theta0 + + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 66.6 105.0 + } + + # Generate a "backbone" 3-body interaction whenever 3 atoms are bonded + # together. We do this by to asking moltemplate to generate this + # 3-body interaction whenever 3 consecutively bonded atoms satisfy + # the following type requirement: + # + # angleType atomtypes1 2 3 bondtypes1 2 + + write_once("Data Angles By Type") { + @angle:backbone * * * * * + } + + + + + + # 4-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Udihedral(phi) = K * (1 + cos(n*phi - d)) + # + # The d parameter is in degrees, K is in kcal/mol/rad^2. + # + # The corresponding command is: + # + # dihedral_coeff dihedralType dihedralstylename K n d w + # ("w" is the weight for 1-4 pair interactions, which we set to 0) + + write_once("In Settings") { + dihedral_coeff @dihedral:turn charmm 0.2 3 0 0 + dihedral_coeff @dihedral:term3 charmm 1.2 3 0 0 + + dihedral_coeff @dihedral:delta65_0 charmm 1.2 1 -65 0 + dihedral_coeff @dihedral:delta62_5 charmm 1.2 1 -62 0 + dihedral_coeff @dihedral:delta60_0 charmm 1.2 1 -60 0 + dihedral_coeff @dihedral:delta57_5 charmm 1.2 1 -57 0 + dihedral_coeff @dihedral:delta55_0 charmm 1.2 1 -55 0 + } + + #write_once("In Settings") { + # dihedral_coeff @dihedral:turn charmm 0.2 3 0.0 0 + # dihedral_coeff @dihedral:term3 charmm 1.2 3 0.0 0 + # dihedral_coeff @dihedral:delta65_0 charmm 1.2 1 -65.0 0 + # dihedral_coeff @dihedral:delta62_5 charmm 1.2 1 -62.5 0 + # dihedral_coeff @dihedral:delta60_0 charmm 1.2 1 -60.0 0 + # dihedral_coeff @dihedral:delta57_5 charmm 1.2 1 -57.5 0 + # dihedral_coeff @dihedral:delta55_0 charmm 1.2 1 -55.5 0 + #} + + # Generate 4-body interactions whenever 4 consecutively bonded atoms satisfy + # the following type requirements: + + write_once("Data Dihedrals By Type") { + # The dihedral interaction between backbone atoms in the helix or sheet-like + # regions is proportional to the sum of two terms: cos(phi+delta)+cos(3*phi) + # where delta is a constant used to control the bias between helices/sheets. + # As of 2013-4-07, the "fourier", "table", "class2", and "charmm", + " dihedral_styles can implement this potential. + # However dihedral_style "charmm" can only handle one cosine term at a time. + # So we use two commands to create two dihedral interactions for the same + # set of of four atoms ("cos3" and "delta60_0"). (To allow the + # superposition of multiple dihedral interactions on the same atoms, + # be sure to run moltemplate with the "-overlay-dihdedrals" argument.) + # + # dihedralType atomtypes1 2 3 4 bondtypes1 2 3 + + @dihedral:term3 @atom:H @atom:L @atom:H @atom:L * * * + @dihedral:delta60_0 @atom:H @atom:L @atom:H @atom:L * * * + + @dihedral:term3 @atom:H @atom:L @atom:L @atom:H * * * + @dihedral:delta60_0 @atom:H @atom:L @atom:L @atom:H * * * + + @dihedral:term3 @atom:L @atom:H @atom:H @atom:L * * * + @dihedral:delta60_0 @atom:L @atom:H @atom:H @atom:L * * * + + @dihedral:term3 @atom:H @atom:H @atom:L @atom:L * * * + @dihedral:delta60_0 @atom:H @atom:H @atom:L @atom:L * * * + + # Comment out the next 4 lines: (They are redundant with the lines above) + #@dihedral:term3 @atom:L @atom:L @atom:H @atom:H * * * + #@dihedral:delta60_0 @atom:L @atom:L @atom:H @atom:H * * * + #@dihedral:term3 @atom:L @atom:H @atom:L @atom:H * * * + #@dihedral:delta60_0 @atom:L @atom:H @atom:L @atom:H * * * + # (Redundant: The LLHH pattern is identical to HHLL after order reversal) + # (Redundant: The LHLH pattern is identical to HLHL after order reversal) + + # Right now the dihedral-angle settings are "unfrustrated", meaning that the + # peptide backbone is equally happy to adopt helical or sheet-like secondary + # structure (See Table IV of Bellesia et. al, Prot Sci, 19, 141 (2010)). + # You can change that by changing "delta60_0" to one of the other choices. + + # Any dihedral interactions containing "N" atoms use the @dihedral:turn + # interaction (which is much weaker). + @dihedral:turn @atom:N @atom:* @atom:* @atom:* * * * + @dihedral:turn @atom:N @atom:N @atom:* @atom:* * * * + @dihedral:turn @atom:N @atom:N @atom:N @atom:* * * * + @dihedral:turn @atom:N @atom:N @atom:N @atom:N * * * + # Comment out the next 4 lines: (They are redundant with the lines above) + # @dihedral:turn @atom:N @atom:N @atom:N @atom:N * * * + # @dihedral:turn @atom:* @atom:N @atom:N @atom:N * * * + # @dihedral:turn @atom:* @atom:* @atom:N @atom:N * * * + # @dihedral:turn @atom:* @atom:* @atom:* @atom:N * * * + } + +} # 1beadProtSci2010 (namespace) + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/class2/1beadProtSci2010.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/class2/1beadProtSci2010.lt new file mode 100644 index 0000000000..a0e305f844 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/class2/1beadProtSci2010.lt @@ -0,0 +1,385 @@ +# This file defines a family of coarse-grained protein models used in: +# G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) +# +# +# For portability, all definitions in this file are enclosed within +# the "1beadProtSci2010" namespace. To access them, put +# "using namespace 1beadProtSci2010" in your LT file. + +# Strategy: +# +#1) First I'll define some building blocks +# (short helices, sheets and turns of a predetermined length) +# +#2) Then I'll cut and paste them together to build +# a 4-helix bundle or a 4-strand beta-barrel. +# +# Doing it this way is optional. It's simpler (but longer) to simply write +# out the entire sequence of all 73 atoms in a single "Data Atoms" section. +# (IE. Don't try to subdivide it.) It's also simpler to explicitly list the +# 72 bonds, 71 3-body angles and 70 4-body dihedral angle interactions +# manually (instead of inferring them from the atom type). If your protein +# has helices which are not identical, this would probably be easier. +# Use whichever style you prefer. +# +# +# Note that atom types, bond types, angle types, and dihedral types +# are shared between all molecules defined in the "1beadProtSci2010" family. +# (That's why there is a "../" in their path-names. Otherwise atom, bond, +# angle types, etc... are not shared between different molecules.) +# +# Confusing detail: +# Each molecule in LAMMPS can be assigned a unique molecule-ID (an integer). +# These are represented by the "$mol" variable written next to each atom. +# Our protein has multiple subunits (in this case: helices, sheets, turns). +# Because we want the subunits to share the same molecule-ID counter we use +# "$mol:..." instead of "$mol" which tells moltemplate to search for the +# parent molecule's ID. This is optional. If it bothers you, just use "$mol" + + + +1beadProtSci2010 { + + write_once("In Init") { + # -- Default styles for "1beadProtSci2010" -- + units lj + atom_style full + # (Hybrid force fields were not necessary but are used for portability.) + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid class2 + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 rsoftcore 1 + + # If charges are needed, (assuming biopolymers), try one of: + #dielectric 80.0 + #pair_style hybrid lj/cut/coul/debye 0.1 4.0 + # or (for short distances, below a couple nm) + #pair_style hybrid lj/charmm/coul/charmm/implicit 3.5 4.0 + + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + + + # ---- Building blocks: A16, B16, Turn3 ---- + + # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each) + + A16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../L 0.0 -0.4 -0.4 0.0 + $atom:a2 $mol:... @atom:../L 0.0 0.4 -0.4 0.6 + $atom:a3 $mol:... @atom:../H 0.0 0.4 0.4 1.2 + $atom:a4 $mol:... @atom:../H 0.0 -0.4 0.4 1.8 + $atom:a5 $mol:... @atom:../L 0.0 -0.4 -0.4 2.4 + $atom:a6 $mol:... @atom:../L 0.0 0.4 -0.4 3.0 + $atom:a7 $mol:... @atom:../H 0.0 0.4 0.4 3.6 + $atom:a8 $mol:... @atom:../H 0.0 -0.4 0.4 4.2 + $atom:a9 $mol:... @atom:../L 0.0 -0.4 -0.4 4.8 + $atom:a10 $mol:... @atom:../L 0.0 0.4 -0.4 5.4 + $atom:a11 $mol:... @atom:../H 0.0 0.4 0.4 6.0 + $atom:a12 $mol:... @atom:../H 0.0 -0.4 0.4 6.6 + $atom:a13 $mol:... @atom:../L 0.0 -0.4 -0.4 7.2 + $atom:a14 $mol:... @atom:../L 0.0 0.4 -0.4 7.8 + $atom:a15 $mol:... @atom:../H 0.0 0.4 0.4 8.4 + $atom:a16 $mol:... @atom:../H 0.0 -0.4 0.4 9.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # A16 + + + # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each) + + B16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../L 0.0 -0.3 0.0 0.0 + $atom:a2 $mol:... @atom:../H 0.0 0.3 0.0 0.8 + $atom:a3 $mol:... @atom:../L 0.0 -0.3 0.0 1.6 + $atom:a4 $mol:... @atom:../H 0.0 0.3 0.0 2.4 + $atom:a5 $mol:... @atom:../L 0.0 -0.3 0.0 3.2 + $atom:a6 $mol:... @atom:../H 0.0 0.3 0.0 4.0 + $atom:a7 $mol:... @atom:../L 0.0 -0.3 0.0 4.8 + $atom:a8 $mol:... @atom:../H 0.0 0.3 0.0 5.6 + $atom:a9 $mol:... @atom:../L 0.0 -0.3 0.0 6.4 + $atom:a10 $mol:... @atom:../H 0.0 0.3 0.0 7.2 + $atom:a11 $mol:... @atom:../L 0.0 -0.3 0.0 8.0 + $atom:a12 $mol:... @atom:../H 0.0 0.3 0.0 8.8 + $atom:a13 $mol:... @atom:../L 0.0 -0.3 0.0 9.6 + $atom:a14 $mol:... @atom:../H 0.0 0.3 0.0 10.4 + $atom:a15 $mol:... @atom:../L 0.0 -0.3 0.0 11.2 + $atom:a16 $mol:... @atom:../H 0.0 0.3 0.0 12.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # B16 + + T3 { # T3 is a "turn" region consisting of 3 beads + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../N 0.0 -0.8 0.0 0.0 + $atom:a2 $mol:... @atom:../N 0.0 0.0 0.55 -0.24 + $atom:a3 $mol:... @atom:../N 0.0 0.8 0.0 0.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + } + + } # T3 + + # (Note: Again, atom types, bond-types, (dihedral-types, any variable, etc) + # can be shared. The ".." in "@atom:../CA" tells moltemplate that + # atom type CA is defined in the parent's environment. (We are + # sharing the CA atom type between both the H and P residues. + # The same is true of the ".." in "@bond:../sidechain". + # + # + # Note: The "..." in "$mol:..." tells moltemplate that this molecule may + # be a part of a larger molecule, and (if so) to use the larger + # molecule's id number as it's own. + + + + # ----- Now build larger molecules using A16, B16 and T3 ------- + + 4HelixBundle { + + helix1 = new A16.rot( -45, 0,0,1).move(-1.12691645,-1.12691645, 0) + helix2 = new A16.rot( 45, 0,0,1).move( 1.12691645,-1.12691645, 0) + helix3 = new A16.rot( 135, 0,0,1).move( 1.12691645, 1.12691645, 0) + helix4 = new A16.rot( 225, 0,0,1).move(-1.12691645, 1.12691645, 0) + # Note: 1.12691645 ~= 0.5*2^(1/6) + 0.4*sqrt(2) + + turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-0.2,-0.7,9.9) + turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(0.7,-0.15,-0.3) + turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(0.2,0.7,9.9) + + # Note: In the paper, this is described as the "UA2" conformation + # (I played around with the angles until it looked "okay". This is not + # the minimum energy conformation. Further minimization is necessary.) + + # Now bond the pieces together. + # (Note: angle & dihedral interactions will be generated automatically.) + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # <-- create a variable for the parent's Molecule-ID + } + + 4SheetBundle { + + sheet1 = new B16.rot( 45, 0,0,1).move(-0.793700526,-0.793700526, 0) + sheet2 = new B16.rot( 135, 0,0,1).move( 0.793700526,-0.793700526, 0) + sheet3 = new B16.rot( 225, 0,0,1).move( 0.793700526, 0.793700526, 0) + sheet4 = new B16.rot( 315, 0,0,1).move(-0.793700526, 0.793700526, 0) + # Note: 0.793700526 ~= 0.5*2^(1/6) * sqrt(1/2) + + turn1 = new T3.rot(180,1,0,0).rot(0,0,0,1).move(0,-1.3,12.6) + turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(0.7,-0.0,-0.9) + turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move(0,1.3,12.6) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + } + + + # There are 3 atom types (referred to above as ../H, ../L, and ../N) + # Define their masses: + + write_once("Data Masses") { + @atom:H 1.0 + @atom:L 1.0 + @atom:N 1.0 + + } + + + + # -------------------------------------------------------------------- + # -- In this example, all force field parameters are stored in the -- + # -- file named "In Settings". They can also go in sections like -- + # -- "Data Pair Coeffs", "Data Bond Coeffs", "Data Angle Coeffs"... -- + # -------------------------------------------------------------------- + + + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:H @atom:H lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 0 0 0 0 + pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 1.0 1.0 1 0 0 0 0 0 + pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 1.0 1.0 1 0 0 0 0 0 + } + # (Interactions between different atom types use "arithmetic" + # and "maxmax" ("repulsion-wins") mixing rules.) + + + # 2-body (bonded) interactions: + # + # Ubond(r) = (k/2)*(r-0)^2 + # + # The corresponding command is: + # + # bond_coeff bondType bondstylename k r0 + # + + write_once("In Settings") { + bond_coeff @bond:backbone harmonic 66.6 1.0 + } + + + + # 3-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Uangle(theta) = (k/2)*(theta-theta0)^2 + # (k in kcal/mol/rad^2, theta0 in degrees) + # + # The corresponding command is: + # + # angle_coeff angleType anglestylename k theta0 + + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 66.6 105.0 + } + + # Generate a "backbone" 3-body interaction whenever 3 atoms are bonded + # together. We do this by to asking moltemplate to generate this + # 3-body interaction whenever 3 consecutively bonded atoms satisfy + # the following type requirement: + # + # angleType atomtypes1 2 3 bondtypes1 2 + + write_once("Data Angles By Type") { + @angle:backbone * * * * * + } + + + + + + # 4-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Udihedral(phi) = K * (1 + cos(n*phi - d)) + # + # The d parameter is in degrees, K is in kcal/mol/rad^2. + # + # The corresponding command is: + # + + # From the Bellesia et al paper: Udihedral(x) = 1.2*(cos(x+delta) + cos(3x)) (delta=60) + # (scratchwork: 1.2*cos(x+60) = -1.2*cos(x+60-180) = -1.2*cos(x-120)) + # and 1.2*cos(3x) = -1.2*cos(3x-180) + # and 0.2*cos(x) = -0.2*cos(x - 180) + # This way, the energies match exactly with the implementation using charmm dihedrals.) + # + # dihedralType dihedralstylename K1 phi1 K2 phi2 K3 phi3 + + write_once("In Settings") { + dihedral_coeff @dihedral:delta60_0 class2 1.2 120.0 0 0 1.2 180.0 + dihedral_coeff @dihedral:turn class2 0 0 0 0 0.2 180.0 + + # All of the cross-terms (for the class2 force-field) are zero (see docs): + dihedral_coeff @dihedral:delta60_0 class2 mbt 0 0 0 0 + dihedral_coeff @dihedral:delta60_0 class2 ebt 0 0 0 0 0 0 0 0 + dihedral_coeff @dihedral:delta60_0 class2 at 0 0 0 0 0 0 0 0 + dihedral_coeff @dihedral:delta60_0 class2 aat 0 0 0 + dihedral_coeff @dihedral:delta60_0 class2 bb13 0 0 0 + dihedral_coeff @dihedral:turn class2 mbt 0 0 0 0 + dihedral_coeff @dihedral:turn class2 ebt 0 0 0 0 0 0 0 0 + dihedral_coeff @dihedral:turn class2 at 0 0 0 0 0 0 0 0 + dihedral_coeff @dihedral:turn class2 aat 0 0 0 + dihedral_coeff @dihedral:turn class2 bb13 0 0 0 + } + + # Generate 4-body interactions whenever 4 consecutively bonded atoms satisfy + # the following type requirements: + + write_once("Data Dihedrals By Type") { + # dihedralType atomtypes1 2 3 4 bondtypes1 2 3 + + @dihedral:delta60_0 @atom:H @atom:L @atom:H @atom:L * * * + @dihedral:delta60_0 @atom:H @atom:H @atom:L @atom:L * * * + @dihedral:delta60_0 @atom:H @atom:L @atom:L @atom:H * * * + @dihedral:delta60_0 @atom:L @atom:H @atom:H @atom:L * * * + + @dihedral:turn @atom:N @atom:* @atom:* @atom:* * * * + @dihedral:turn @atom:N @atom:N @atom:* @atom:* * * * + @dihedral:turn @atom:N @atom:N @atom:N @atom:* * * * + @dihedral:turn @atom:N @atom:N @atom:N @atom:N * * * + + #### Comment out the next 6 lines: (They are redundant with the lines above) + ## @dihedral:delta60_0 @atom:L @atom:H @atom:L @atom:H * * * + ## @dihedral:delta60_0 @atom:L @atom:L @atom:H @atom:H * * * + ## @dihedral:turn @atom:N @atom:N @atom:N @atom:N * * * + ## @dihedral:turn @atom:* @atom:N @atom:N @atom:N * * * + ## @dihedral:turn @atom:* @atom:* @atom:N @atom:N * * * + ## @dihedral:turn @atom:* @atom:* @atom:* @atom:N * * * + ################################################################### + } + + +} # 1beadProtSci2010 (namespace) + diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt new file mode 100644 index 0000000000..fcc6188f71 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt @@ -0,0 +1,25 @@ +import "1beadProtSci2010.lt" + +using namespace 1beadProtSci2010 + +prot = new 4HelixBundle + +write_once("Data Boundary") { + 0 100 xlo xhi + 0 100 ylo yhi + 0 100 zlo zhi +} + + + + +# ------------ Note: ------------- +# +# If you want to try the version using "CHARMM" dihedrals, import this instead: +# +# import "versions_with_comments/1beadProtSci2010_charmm.lt" +# +# (The two versions should behave identically. However by overlaying +# dihedral interactions on top of eachother, charmm allows you to construct +# a Fourier series with an arbitrary number of terms. Class2 stops at 3. +# This is useful if one day you want to use a more complex dihedral potential.) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/run.in.min b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/run.in.min new file mode 100644 index 0000000000..fce9843aa8 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/run.in.min @@ -0,0 +1,19 @@ +# -- Init section -- + +include system.in.init + +# -- Atom definition section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run section -- + +dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz + +minimize 1.0e-5 1.0e-7 500 2000 + +write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/run.in.nvt new file mode 100644 index 0000000000..f1a7aa6540 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/run.in.nvt @@ -0,0 +1,44 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +# I you want to be careful, you can minimize the system first. (Try using +# "run.in.min" and uncomment the read_restart command in this file below.) +# read_restart system_after_min.rst + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 0.008 +dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz + +# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". +# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) + +fix fxlan all langevin 0.4 0.4 1.0 48279 +fix fxnve all nve + +# Notes: +# The temperature is in reduced units and is set to 0.4. +# The inverse-damping-rate "damp" (which has units of time) is set to 1.0. +# (See http://lammps.sandia.gov/doc/fix_langevin.html) + + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo_modify norm no #(report total energy not energy / num_atoms) +thermo 500 #(time interval for printing out "thermo" data) + +restart 10000000 restart_nvt + +run 1000000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/README.TXT b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/README.TXT new file mode 100644 index 0000000000..305d00d636 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/README.TXT @@ -0,0 +1,114 @@ + This example shows how to build a multicomponent spherical vesicle. + The lipid bilayer is composed of two different lipids (DPPC and DLPC). + The vesicle also contains trans-membrane protein inclusions. + + The coordinates for the vesicle are constructed by PACKMOL (see below). + + The DPPC lipid model is described here: + G. Brannigan, P.F. Philips, and F.L.H. Brown, + Physical Review E, Vol 72, 011915 (2005) + (The DLPC model is a truncated version of DPPC. Modifications discussed below.) + The protein model is described here: + G. Bellesia, AI Jewett, and J-E Shea, + Protein Science, Vol19 141-154 (2010) + +--- PREREQUISITES: --- + +1) This example requires PACKMOL. You can download PACKMOL here: + + http://www.ime.unicamp.br/~martinez/packmol/ + + (Moltemplate does not come with an easy way to generate spherically-symmetric + structures, so I used the PACKMOL program to move the molecules into position.) + +2) This example requires the "dihedral_style fourier", which is currently +in the USER-MISC package. Build LAMMPS with this package enabled using + make yes-user-misc +before compiling LAMMPS. +(See http://lammps.sandia.gov/doc/Section_start.html#start_3 for details.) + +3) This example may require additional features to be added to LAMMPS. +If LAMMPS complains about an "Invalid pair_style", then + a) download the "additional_lammps_code" from + http://moltemplate.org (upper-left corner menu) + b) unpack it + c) copy the .cpp and .h files to the src folding of your lammps installation. + d) (re)compile LAMMPS. + +------ Details ------- + +This example contains a coarse-grained model of a 4-helix bundle protein +inserted into a lipid bilayer (made from a mixture of DPPC and DLPC). + + -- Protein Model: -- + +The coarse-grained protein is described in: + G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) +Here we use the "AUF2" model described in that paper. +(The hydrophobic beads face outwards.) + + -- Memebrane Model: -- + +The DPPC lipid bilayer described in: + G. Brannigan, P.F. Philips, and F.L.H. Brown, + Physical Review E, Vol 72, 011915 (2005) +and: + M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown + J. Chem. Phys. 135, 244701 (2011) + +As in Watson(JCP 2011), rigid bond-length constraints +have been replaced by harmonic bonds. + +A truncated version of this lipid (named "DLPC") has also been added. +The bending stiffness of each lipid has been increased to compensate +for the additional disorder resulting from mixing two different types +of lipids together. (Otherwise pores appear.) +Unlike the original "DPPC" molecule model, the new "DPPC" and "DLPC" models +have not been carefully parameterized to reproduce the correct behavior in +a lipid bilayer mixture. + + -- Interactions between the proteins and lipids -- + +This is discussed in the "system.lt" file. + +--- Building the files necessary to run a simulation in LAMMPS --- + +step 1) Run PACKMOL + + Type these commands into the shell. + (Each command could take several hours.) + +cd packmol_files + packmol < step1_proteins.inp # This step determines the protein's location + packmol < step2_innerlayer.inp # this step builds the inner monolayer + packmol < step3_outerlayer.inp # this step builds the outer monolayer +cd .. + +step 2) Run MOLTEMPLATE + Type these commands into the shell. + (This could take up to 10 minutes.) + +cd moltemplate_files + moltemplate.sh system.lt -xyz ../system.xyz + mv -f system.in* system.data ../ + cp -f table_int.dat ../ +cd .. + +--- Running LAMMPS --- + +step3) Run LAMMPS: + Type these commands into the shell. + (This could take days.) + +lmp_linux -i run.in.min # Minimize the system (important, and very slow) + +lmp_linux -i run.in.nvt # Run a simulation at constant volume + +If you have compiled the MPI version of lammps, you can run lammps in parallel: + +mpirun -np 4 lmp_linux -i run.in.min + or +mpirun -np 4 lmp_linux -i run.in.nvt + +(Assuming you have 4 cores, for example.) + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/README_run.sh new file mode 100755 index 0000000000..99f39891e4 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/README_run.sh @@ -0,0 +1,24 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The "run.in.nvt" file is a LAMMPS input script containing +# references to the input scripts and data files +# you hopefully have created earlier with MOLTEMPLATE and PACKMOL: +# system.in.init, system.in.settings, system.in.coords, system.data, +# and table_int.dat +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + +lmp_linux -i run.in.min # Minimize the system (important, and very slow) + +lmp_linux -i run.in.nvt # Run a simulation at constant volume + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.min +#or +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/README_setup.sh new file mode 100755 index 0000000000..0764f02f30 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/README_setup.sh @@ -0,0 +1,50 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + +# First, generate the coordinates (the "system.xyz" file) this way +# (This can be a very slow process.) +cd packmol_files + + # You must run each packmol commend one after the other + # NOTE: If PACKMOL gets stuck in an endless loop, then edit the corresponding + # "inp" file. This should not happen. You can also usually interrupt + # packmol after 30 minutes, and the solution at that point should be good + # enough for use. + packmol < step1_proteins.inp # This step determines the protein's location + # It takes ~20 minutes (on an intel i7) + packmol < step2_innerlayer.inp # this step builds the inner monolayer + # It takes ~90 minutes + packmol < step3_outerlayer.inp # this step builds the outer monolayer + # It takes ~4 hours + + # Running these three commands will probably take about an hour. + # (It depends on how uniformly you need the packing to be.) + + mv -f step3_outerlayer.xyz ../system.xyz +cd .. + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt -xyz ../system.xyz + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # The "table_int.dat" file contains tabular data for the lipid INT-INT atom + # 1/r^2 interaction. We need it too. (This slows down the simulation by x2, + # so I might look for a way to get rid of it later.) + cp -f table_int.dat ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/images/vesicle_hole_blackbk_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/images/vesicle_hole_blackbk_LR.jpg new file mode 100644 index 0000000000..843a8f2d83 Binary files /dev/null and b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/images/vesicle_hole_blackbk_LR.jpg differ diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/1beadProtSci2010.lt b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/1beadProtSci2010.lt new file mode 100644 index 0000000000..d2aa805a5b --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/1beadProtSci2010.lt @@ -0,0 +1,233 @@ +# This file defines a 4-helix bundle coarse-grained protein model (AUF2) used in +# G. Bellesia, AI Jewett, and J-E Shea, +# Protein Science, Vol19 141-154 (2010) +# +# Strategy: +# +#1) First I'll define some building blocks (A16, B16, T3) +# which are helices, sheets and turns of a predetermined length) +# +#2) Then I'll copy and paste them together to build +# a 4-helix bundle (or a 4-strand beta-barrel). +# This approach is optional. If your protein has helices which are not +# identical, you should probably just include all 4 helices in a single +# "Data Atoms" section and don't try to subdivide the protein into pieces.) + + + +1beadProtSci2010 { # <-- enclose definitions in a namespace for portability + + # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each) + + A16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../sL 0.0 -2.4 -2.4 0.0 + $atom:a2 $mol:... @atom:../sL 0.0 2.4 -2.4 3.6 + $atom:a3 $mol:... @atom:../sH 0.0 2.4 2.4 7.2 + $atom:a4 $mol:... @atom:../sH 0.0 -2.4 2.4 10.8 + $atom:a5 $mol:... @atom:../sL 0.0 -2.4 -2.4 14.4 + $atom:a6 $mol:... @atom:../sL 0.0 2.4 -2.4 18.0 + $atom:a7 $mol:... @atom:../sH 0.0 2.4 2.4 21.6 + $atom:a8 $mol:... @atom:../sH 0.0 -2.4 2.4 25.2 + $atom:a9 $mol:... @atom:../sL 0.0 -2.4 -2.4 28.8 + $atom:a10 $mol:... @atom:../sL 0.0 2.4 -2.4 32.4 + $atom:a11 $mol:... @atom:../sH 0.0 2.4 2.4 36.0 + $atom:a12 $mol:... @atom:../sH 0.0 -2.4 2.4 39.6 + $atom:a13 $mol:... @atom:../sL 0.0 -2.4 -2.4 43.2 + $atom:a14 $mol:... @atom:../sL 0.0 2.4 -2.4 46.8 + $atom:a15 $mol:... @atom:../sH 0.0 2.4 2.4 50.4 + $atom:a16 $mol:... @atom:../sH 0.0 -2.4 2.4 54.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # A16 + + + T3 { # T3 is a "turn" region consisting of 3 beads + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../tN 0.0 -4.8 0.0 0.0 + $atom:a2 $mol:... @atom:../tN 0.0 0.0 3.3 -1.44 + $atom:a3 $mol:... @atom:../tN 0.0 4.8 0.0 0.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + } + + } # T3 + + + # ----- Now build a larger molecule using A16 and T3 ------- + + # Create a 4-Helix bundle. + # In this version, the hydrophobic beads are poing outward. + # I oriented them this way because I want to place this protein in a membrane. + # (There is another file in this directory containing alternate version + # of this same molecule with the hydrophobic beads pointing inward.) + + 4HelixInsideOut { + helix1 = new A16.rot(-225, 0,0,1).move(-5.70,-5.70,-32.4) + helix2 = new A16.rot(-135, 0,0,1).move( 5.70,-5.70,-28.8) + helix3 = new A16.rot( -45, 0,0,1).move( 5.70, 5.70,-25.2) + helix4 = new A16.rot( 45, 0,0,1).move(-5.70, 5.70,-21.6) + + turn1 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot( 10,0,0,1).move(0.78,-4.2, 27.9) + turn2 = new T3.rot(-10,1,0,0).rot( 20,0,1,0).rot(-70,0,0,1).move(4.55, 2.4,-33.0) + turn3 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot(190,0,0,1).move(-0.78,4.2, 34.2) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + + } # 4HelixInsideOut + + + # -------- Minor coordinates adjustment: ----------- + + # Those coordinates in the commands above are a little too large. + # To make it easier to type them in, I was using sigma=6.0 Angstroms. + # Instead, here I'll try using sigma=5.5 Angstroms. 5.5/6 = 0.916667) + + 4HelixInsideOut.scale(0.9166666666666666) + + # Note: "scale()" only effects the initial coordinates of + # the molecule, not the force field parameters. + # (If you plan to minimize the molecule, you don't need to + # be so careful about the initial coordinates. In that case, + # you don't have worry about "scale()". Feel free to remove.) + + + + # -------------- Force-Field Parameters ------------ + + # Units and force-field styles for this protein model + # (These can be overridden later.) + + write_once("In Init") { + units real + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid fourier + pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 21.0 24.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) + } + + # --- Distance Units --- + # In this version of the model, sigma (the bond-length + # and particle diameter) is rounded to 5.5 Angstroms. + # + # --- Energy & Temperature Units --- + # In this protein model, "epsilon" represents the free energy + # bonus for bringing two hydrophobic amino acids together. + # Here I choose to set epsilon to 1.806551818181818 kCal/mole. + # This value was chosen so that a temperature of 300 Kelvin lies at + # 0.33 epsilon, which is the unfolding temperature of the marginally stable + # "ASF1" protein model from the Bellesia et al 2010 paper. + # This choice insures that both the "ASF1" model from that paper, + # as well as the much more stable "AUF2" protein we use here (which + # unfolds at 0.42*eps) should definitely remain stable at 300 degrees Kelvin, + # in the bulk at least. (However it's not clear that these energy + # parameters will work well for a protein in membrane. Perhaps I'll + # run some tests and fine tune these parameters for this scenario.) + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) + # + # i j pairstylename eps sig K L + # + write_once("In Settings") { + pair_coeff @atom:sH @atom:sH lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 + pair_coeff @atom:sL @atom:sL lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0 + pair_coeff @atom:tN @atom:tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0 + } + + # The exact value of the bond_coeff does not matter too much as long as + # it is "stiff enough". Here I use a softer bond spring than the one + # used in the paper so that I can increase the time step. + # I also use a relatively soft spring to constrain the bond angles. + + # bond_coeff bondType bondstylename k r0 + + write_once("In Settings") { + bond_coeff @bond:1beadProtSci2010/backbone harmonic 10.0 5.5 + } + + + # angleType atomtypes1 2 3 bondtypes1 2 + + write_once("Data Angles By Type") { + @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* + } + + # angle_coeff angleType anglestylename k theta0 + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 100.0 105.0 + } + + + # dihedralType atomtypes1 2 3 4 bondtypes1 2 3 + + write_once("Data Dihedrals By Type") { + # For a chain of sH and sL atoms, use the @dihedral:delta65_0 + # parameters. (This corresponds to the "AUF2" model from the + # Bellesia et. al 2010 paper.) + + @dihedral:delta65_0 @atom:s* @atom:s* @atom:s* @atom:s* * * * + + # If "tN" (turn) atoms are present, use the @dihedral:turn parameters + + @dihedral:turn @atom:tN @atom:* @atom:* @atom:* * * * + } + + write_once("In Settings") { + dihedral_coeff @dihedral:delta60_0 fourier 2 2.167862 3 0 2.167862 1 -60.0 + dihedral_coeff @dihedral:delta65_0 fourier 2 2.167862 3 0 2.167862 1 -65.0 + dihedral_coeff @dihedral:turn fourier 1 0.361310 3 0 + # Note: 2.167862=1.2*epsilon and 0.361310=0.2*epsilon. + } + + + # --- Mass Units --- + # Typical amino acids weigh approximately 110.0 grams/mole. (Rounding down): + write_once("Data Masses") { + @atom:1beadProtSci2010/sH 100.0 + @atom:1beadProtSci2010/sL 100.0 + @atom:1beadProtSci2010/tN 100.0 + } + +} # 1beadProtSci2010 (namespace) + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/1beadProtSci2010_variations.lt b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/1beadProtSci2010_variations.lt new file mode 100644 index 0000000000..e6e6bced70 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/1beadProtSci2010_variations.lt @@ -0,0 +1,225 @@ +### THIS FILE IS OPTIONAL AND IS NOT NECESSARY. IN THIS FILE, I DEFINED SOME ## +### ADDITIONAL PROTEIN TYPES FROM THE PAPER THAT I DID NOT USE IN THIS EXAMPLE## +# +# This file defines a family of coarse-grained protein models used in: +# G. Bellesia, AI Jewett, and J-E Shea, +# Protein Science, Vol19 141-154 (2010) +# +# Strategy: +# +#1) First I'll define some building blocks (A16, B16, T3) +# which are helices, sheets and turns of a predetermined length) + +import "1beadProtSci2010.lt" + +# We defined A16 and T3 earlier in "1beadPRotSci2010.lt" Will define B16 below +# +#2) Then I'll copy and paste them together to build +# a 4-helix bundle or a 4-strand beta-barrel. + + +1beadProtSci2010 { #<-- Add new molecules to existing namespace defined earlier + # This way we don't have to start from scratch. We can + # use all the atom types and angle settings defined earlier + + # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each) + + B16 { + + # AtomID MoleculeID AtomType Charge X Y Z + + write('Data Atoms') { + $atom:a1 $mol:... @atom:../sL 0.0 -1.8 0.0 0.0 + $atom:a2 $mol:... @atom:../sH 0.0 1.8 0.0 4.8 + $atom:a3 $mol:... @atom:../sL 0.0 -1.8 0.0 9.6 + $atom:a4 $mol:... @atom:../sH 0.0 1.8 0.0 14.4 + $atom:a5 $mol:... @atom:../sL 0.0 -1.8 0.0 19.2 + $atom:a6 $mol:... @atom:../sH 0.0 1.8 0.0 24.0 + $atom:a7 $mol:... @atom:../sL 0.0 -1.8 0.0 28.8 + $atom:a8 $mol:... @atom:../sH 0.0 1.8 0.0 33.6 + $atom:a9 $mol:... @atom:../sL 0.0 -1.8 0.0 38.4 + $atom:a10 $mol:... @atom:../sH 0.0 1.8 0.0 43.2 + $atom:a11 $mol:... @atom:../sL 0.0 -1.8 0.0 48.0 + $atom:a12 $mol:... @atom:../sH 0.0 1.8 0.0 52.8 + $atom:a13 $mol:... @atom:../sL 0.0 -1.8 0.0 57.6 + $atom:a14 $mol:... @atom:../sH 0.0 1.8 0.0 62.4 + $atom:a15 $mol:... @atom:../sL 0.0 -1.8 0.0 67.2 + $atom:a16 $mol:... @atom:../sH 0.0 1.8 0.0 72.0 + } + + write('Data Bonds') { + $bond:b1 @bond:../backbone $atom:a1 $atom:a2 + $bond:b2 @bond:../backbone $atom:a2 $atom:a3 + $bond:b3 @bond:../backbone $atom:a3 $atom:a4 + $bond:b4 @bond:../backbone $atom:a4 $atom:a5 + $bond:b5 @bond:../backbone $atom:a5 $atom:a6 + $bond:b6 @bond:../backbone $atom:a6 $atom:a7 + $bond:b7 @bond:../backbone $atom:a7 $atom:a8 + $bond:b8 @bond:../backbone $atom:a8 $atom:a9 + $bond:b9 @bond:../backbone $atom:a9 $atom:a10 + $bond:b10 @bond:../backbone $atom:a10 $atom:a11 + $bond:b11 @bond:../backbone $atom:a11 $atom:a12 + $bond:b12 @bond:../backbone $atom:a12 $atom:a13 + $bond:b13 @bond:../backbone $atom:a13 $atom:a14 + $bond:b14 @bond:../backbone $atom:a14 $atom:a15 + $bond:b15 @bond:../backbone $atom:a15 $atom:a16 + } + + } # B16 + + # ----- Now build larger molecules using B16 and T3 ------- + + + 4SheetBarrel { + sheet1 = new B16.rot( 45, 0,0,1).move(-4.762203156,-4.762203156, -36.0) + sheet2 = new B16.rot( 135, 0,0,1).move( 4.762203156,-4.762203156, -36.0) + sheet3 = new B16.rot( 225, 0,0,1).move( 4.762203156, 4.762203156, -36.0) + sheet4 = new B16.rot( 315, 0,0,1).move(-4.762203156, 4.762203156, -36.0) + + turn1 = new T3.rot(180,1,0,0).rot( 0, 0,0,1).move( 0, -7.8, 39.6) + turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(4.2, 0.0,-41.4) + turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move( 0, 7.8, 39.6) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + } + + + # Below I define several alternate conformations of the"4HelixBundleInsideOut" + # molecule I defined earlier in "1beadProtSci2010.lt". Same molecule however. + + 4HelixBundle { + helix1 = new A16.rot( -45, 0,0,1).move(-5.70,-5.70,-32.4) + helix2 = new A16.rot( 45, 0,0,1).move( 5.70,-5.70,-28.8) + helix3 = new A16.rot( 135, 0,0,1).move( 5.70, 5.70,-25.2) + helix4 = new A16.rot( 225, 0,0,1).move(-5.70, 5.70,-21.6) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + + turn1 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot( 8,0,0,1).move(-3.6,-4.8,28.2) + turn2 = new T3.rot(-5,1,0,0).rot( 21,0,1,0).rot(-100,0,0,1).move(4.2,-0.66,-30.9) + turn3 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot(188,0,0,1).move(3.6,4.8,35.4) + + create_var { $mol } # molecule ID number shared by all atoms in this protein + + } # 4HelixBundle + + + + + # --- alternate conformations (same molecule) ---- + + # In the following version, the helices are oriented in a similar way, + # but they are separated a little further away from eachother. + + 4HelixBundleLoose { + + helix1 = new A16.rot( -45, 0,0,1).move(-6.7347723,-6.7347723, -27.0) + helix2 = new A16.rot( 45, 0,0,1).move( 6.7347723,-6.7347723, -27.0) + helix3 = new A16.rot( 135, 0,0,1).move( 6.7347723, 6.7347723, -27.0) + helix4 = new A16.rot( 225, 0,0,1).move(-6.7347723, 6.7347723, -27.0) + + turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-1.2,-4.2,32.4) + turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(4.2,-0.9,-28.8) + turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(1.2,4.2,32.4) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + } + + + # In following version, the helices are oriented in a similar way, + # but they are separated a little further away from eachother. + + 4HelixInsideOutLoose { + helix1 = new A16.rot(-225, 0,0,1).move(-6.7347723,-6.7347723, -27.0) + helix2 = new A16.rot(-135, 0,0,1).move( 6.7347723,-6.7347723, -27.0) + helix3 = new A16.rot( -45, 0,0,1).move( 6.7347723, 6.7347723, -27.0) + helix4 = new A16.rot( 45, 0,0,1).move(-6.7347723, 6.7347723, -27.0) + + turn1 = new T3.rot(180,1,0,0).rot( 10,0,0,1).move( 0.78,-4.2,28.8) + turn2 = new T3.rot( 70,1,0,0).rot(-70,0,0,1).move( 10.8,2.4,-28.2) + turn3 = new T3.rot(180,1,0,0).rot(190,0,0,1).move(-0.78,4.2,28.8) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + + } # 4HelixInsideOutLoose + + + + + # In the following version, the 4 helices are arranged next to each other, + # side-by-side, in a planar conformation (instead of a compact bundle). + + 4HelixPlanar { + helix1 = new A16.rot(-00, 0,0,1).move(0, 0, -27.0) + helix2 = new A16.rot( 00, 0,0,1).move(14.4, 0, -27.0) + helix3 = new A16.rot(-00, 0,0,1).move(28.8, 0, -27.0) + helix4 = new A16.rot( 00, 0,0,1).move(43.2, 0, -27.0) + + turn1 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move( 4.8, 0, 31.8) + turn2 = new T3.rot( 0,1,0,0).rot(180,0,0,1).move(19.2, 0,-31.8) + turn3 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move(34.6, 0, 31.8) + + write('Data Bonds') { + $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 + $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 + $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 + $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 + $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 + $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 + } + create_var { $mol } # molecule ID number shared by all atoms in this protein + + } # 4HelixPlanar + + + # -------- Minor coordinates adjustment: ----------- + # Those coordinates in the commands above are a little too large. + # To make it easier to type them in, I was using sigma=6.0 Angstroms. + # Instead, here I'll try using sigma=5.5 Angstroms. 5.5/6 = 0.916667) + + 4SheetBarrel.scale(0.9166666666666666) + 4HelixBundle.scale(0.9166666666666666) + 4HelixBundleLoose.scale(0.9166666666666666) + 4HelixInsideOutLoose.scale(0.9166666666666666) + 4HelixPlanar.scale(0.9166666666666666) + + # Note: "scale()" only effects the initial coordinates of + # the molecule, not the force field parameters. + # (If you plan to minimize the molecule, you don't need to + # be so careful about the initial coordinates. In that case, + # you don't have worry about "scale()". Feel free to remove.) + + +} # 1beadProtSci2010 (namespace) + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/CGLipidBr2005.lt b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/CGLipidBr2005.lt new file mode 100644 index 0000000000..3b39048f7e --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/CGLipidBr2005.lt @@ -0,0 +1,198 @@ +# Note: +# +# This example may require additional features to be added to LAMMPS. If +# LAMMPS complains about an "Invalid pair_style", then download copy the +# "additional_lammps_code" from moltemplate.org, unpack it into your LAMMPS +# "src" directory and recompile LAMMPS. +# +# -------- Description -------- +# +# This example contains an implementation of the DPPC lipid bilayer described in +# G. Brannigan, P.F. Philips, and F.L.H. Brown, +# Physical Review E, Vol 72, 011915 (2005) +# and: +# M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown +# J. Chem. Phys. 135, 244701 (2011) +# +# As in Watson(JCP 2011), rigid bond-length constraints have been replaced +# by harmonic bonds. +# +# A truncated version of this lipid (named "DLPC") has also been added. +# Unlike the original "DPPC" molecule model, "DLPC" has not been carefully +# parameterized to reproduce the correct behavior in a lipid bilayer mixture. +# +# Units: +# +# The "epsilon" parameter in their model is approximately 2.75 kJ/mole +# ( = 0.657265774378585 kCal/mole, using 1kCal=4.184kJ) +# The "sigma" parameter corresponds to 7.5 angstroms. + + +CGLipidBr2005 { + + + write_once("In Init") { + # -- Default styles for "CGLipidBr2005" -- + units real + atom_style full + # (Hybrid force field styles were used for portability.) + bond_style hybrid harmonic + + #angle_style hybrid cosine/delta # <- used in the original article + angle_style hybrid harmonic # <- prevents unphysical acute angle turns + # Explanation: + # angle_style cosine/delta: U(theta) = k*(1-cos(theta-theta0)) + # angle_style harmonic: U(theta) = k*(theta-theta0)^2 + + dihedral_style none + improper_style none + pair_style hybrid table linear 1130 & + lj/charmm/coul/charmm/inter es4k4l 14.5 15 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" + + neighbor 2.0 multi # <- perhaps unnecessary + communicate multi # <- perhaps unnecessary + } + + + DPPC { + write("Data Atoms") { + $atom:h $mol:. @atom:head 0.0 0.00 0.00 33.75 # DPPC head atom + $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 26.25 + $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 18.75 + $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 11.25 + $atom:t3 $mol:. @atom:../tail 0.0 1.00 0.00 3.75 + } + write("Data Bonds") { + $bond:b1 @bond:../backbone $atom:h $atom:i + $bond:b2 @bond:../backbone $atom:i $atom:t1 + $bond:b3 @bond:../backbone $atom:t1 $atom:t2 + $bond:b4 @bond:../backbone $atom:t2 $atom:t3 + } + write("Data Angles") { + $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 + $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 + $angle:a3 @angle:../backbone $atom:t1 $atom:t2 $atom:t3 + } + + # Define properties of the local (lipid-specific) atom:head type atom: + write_once("Data Masses") { + @atom:head 200.0 + } + write_once("In Settings") { + pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + } + + } #DPPC + + + DLPC { + write("Data Atoms") { + $atom:h $mol:. @atom:head 0.0 0.00 0.00 30.00 # DLPC head atom + $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 22.50 + $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 15.00 + $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 7.50 + } + write("Data Bonds") { + $bond:b1 @bond:../backbone $atom:h $atom:i + $bond:b2 @bond:../backbone $atom:i $atom:t1 + $bond:b3 @bond:../backbone $atom:t1 $atom:t2 + } + write("Data Angles") { + $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 + $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 + } + # Define properties of the local (lipid-specific) atom:head type atom: + write_once("Data Masses") { + @atom:head 200.0 + } + write_once("In Settings") { + pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + } + } #DLPC + + + # Particles and properties shared by all lipid types: + + write_once("Data Masses") { + @atom:int 200.0 + @atom:tail 200.0 + @atom:head 200.0 #<- Default head type. We may override it later. + } + + write_once("In Settings") { + # -- Default settings/parameters for "CGLipidBr2005" -- + # (Hybrid bond & angle styles were used for portability.) + + # As in Watson(JCP 2011), rigid bond-length constraints + # have been replaced by harmonic bonds. + # The k_theta parameter should lie in between 5*epsilon and 10*epsilon. + bond_coeff @bond:backbone harmonic 116.847 7.5 #<--2*5000*eps/sig^2 + } + + write_once("In Settings") { + # cosine/delta: U(theta) = k*(1-cos(theta-theta0)) + #angle_coeff @angle:backbone cosine/delta 4.60086042 180 #<-- 7*eps + # harmonic: U(theta) = k*(theta-theta0)^2 not (k/2)*(theta-theta0)^2 + angle_coeff @angle:backbone harmonic 9.85898661 180 #<-->30*eps + } + # I use a stiffer bond-angle than the original Brannigan & Brown 2005 paper + # to attempt to compensate for the fact that here we are using a lipid + # mixture of DPPC and DLPC. (The mixture of lipids introduces a great deal + # of disorder into the bilayer which would not be present in a DPPC bilayer. + # This causes pores to form. Increasing the angle stiffness prevents this.) + + write_once("In Settings") { + + # The interaction of "atom:int" with other "atom:int" atoms is given by + # epsilon*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2), shifted and cutoff at + # r=3*sigma. This was implemented using pair_style table. + # Unfortunately, mixing lj/charmm and "table" pair styles in the same + # simulation is very inneficient. + + pair_coeff @atom:int @atom:int table table_int.dat INT + + # The interaction of tail beads with eachother is given by the formula below + # and with other atoms ...using Lorenz-Berthelot and "repulsive wins" rules: + # epsilon*(0.4*(sigma/r)^12 - 1.0*(sigma/r)^6), + pair_coeff @atom:tail @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 + pair_coeff @atom:int @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 + + # The interaction of head beads which all other beads is given by: + # epsilon*(0.4*(sigma/r)^12 - 0.0*(sigma/r)^6), + + pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + + } # write_once("In Settings") + + # Note: I divided epsilon by 4 to get "0.1643" because we are using the + # "es4k4l" coeffstyle, corresponding to U(r)=eps(4*K*(s/r)^12 + 4*L*(s/r)^6) + # (The "es4k4l" coeffstyle is the default.) Using this convention makes it + # easier to mix this coarse-grained lipid model with other molecular models. + + + +} # CGLipidBr2005 + + + + + + + + +# Note: This example has not been optimized for speed. +# +# Unfortunately, using both lj/charmm and "table" pair styles in the same +# simulation seems to be very inneficient. (The simulation is twice as slow +# as using only the "lj/charmm" pair styles for every pairwise interaction, +# ...and about 25% slower than using "table" for every pairwise interaction. +# However the lennard-jones pair styles support mixing, so we use them to +# make it easier to run these molecules with other molecules which don't use +# pair_table. I felt that portability was worth the extra 25% slow down.) + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/README.sh b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/README.sh new file mode 100755 index 0000000000..b0de637379 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/README.sh @@ -0,0 +1,22 @@ +# This example shows how to build a multicomponent spherical vesicle. +# The lipid bilayer is composed of two different lipids (DPPC and DLPC), +# The vesicle contains 120 trans-membrane protein inclusions. +# +# ---------------- Prerequisites: ------------------ +# You must run packmol to generate the coordinates beforehand. +# Afterwards, move and rename the final coordinate file to "../system.xyz" +# To do this, check the README.sh file in the ../packmol_files directory. +# (or follow these instructions below) +# +# cd ../packmol_files +# packmol < step1_proteins.inp +# packmol < step2_innerlayer.inp +# packmol < step3_outerlayer.inp +# cp step3_outerlayer.xyz ../system.xyz +# +# These steps could take a few hours. +# +# --- After you have done that, you can run moltemplate using this command: --- + +moltemplate.sh system.lt -xyz ../system.xyz + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py new file mode 100755 index 0000000000..1eb97e6454 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py @@ -0,0 +1,34 @@ +#!/usr/bin/env python + +# Calculate a table of pairwise energies and forces between "INT" atoms +# in the lipid membrane model described in +# Brannigan et al, Phys Rev E, 72, 011915 (2005) +# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) +# However it is truncated at rc2 = 22.5 (shifted upwards to maintain continuity) + +# The previous version included the repulsive core term +def U(r, eps, sigma): + return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) +def F(r, eps, sigma): + return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) +# We don't want to do that. Instead compute the core repulsion using a +# different pair_style and add the attractive term on top of it using the table. +# This way it the core repulsion acts as a default interaction with other atom +# types (using the new repulsive mixing rules). + +epsilon = 2.75/4.184 # kCal/mole +sigma = 7.5 +Rmin = 0.02 +Rmax = 22.6 +rcut = 22.5 +N = 1130 + +for i in range(0,N): + r = Rmin + i*(Rmax-Rmin)/(N-1) + U_r = U(r, epsilon, sigma) - U(rcut, epsilon, sigma) + F_r = F(r, epsilon, sigma) + if r > rcut: + U_r = 0.0 + F_r = 0.0 + print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py new file mode 100755 index 0000000000..32147e444a --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py @@ -0,0 +1,70 @@ +#!/usr/bin/env python + +# Calculate a table of pairwise energies and forces between "INT" atoms +# in the lipid membrane model described in +# Brannigan et al, Phys Rev E, 72, 011915 (2005) +# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) +# I realized later this is not what we want because although energy is conserved +# all enrgies are shifted with respect to energies used in the Brannigan paper +# (by 0.27 kCal/mole) and the later Watson JCP 2011 paper (by 0.224 kCal/mole). +# (So don't use this.) + +# Calculate and print a + +def S(r, rc1, rc2, derivative=False): + """ + Calculate the switching function S(r) which decays continuously + between 1 and 0 in the range from rc1 to rc2 (rc2>rc1): + S(r) = (rc2^2 - r^2)^2 * (rc2^2 + 2*r^2 - 3*rc1^2) / (rc2^2-rc1^2)^3 + I'm using the same smoothing/switching cutoff function used by the CHARMM + force-fields. (I'm even using the same code to implement it, taken + from lammps charmm/coul/charmm pair style, rewritten in python.) + + """ + assert(rc2>rc1) + rsq = r*r + rc1sq = rc1*rc1 + rc2sq = rc2*rc2 + denom_lj_inv = (1.0 / ((rc2sq-rc1sq)* + (rc2sq-rc1sq)* + (rc2sq-rc1sq))) + if rsq > rc2sq: + return 0.0 + elif rsq < rc1sq: + if derivative: + return 0.0 + else: + return 1.0 + else: + rc2sq_minus_rsq = (rc2sq - rsq) + rc2sq_minus_rsq_sq = rc2sq_minus_rsq * rc2sq_minus_rsq + if derivative: + return (12.0 * rsq * rc2sq_minus_rsq * (rsq-rc1sq) * denom_lj_inv) + else: + return (rc2sq_minus_rsq_sq * + (rc2sq + 2.0*rsq - 3.0*rc1sq) * denom_lj_inv) + + +def U(r, eps, sigma): + return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) + +def F(r, eps, sigma): + return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) + +epsilon = 2.75/4.184 # kCal/mole +sigma = 7.5 +Rmin = 0.02 +Rmax = 22.6 +Rc1 = 22.0 +Rc2 = 22.5 +N = 1130 + +for i in range(0,N): + r = Rmin + i*(Rmax-Rmin)/(N-1) + U_r = U(r, epsilon, sigma) + F_r = F(r, epsilon, sigma) + # Multiply U(r) & F(r) by the smoothing/switch function + U_r = U_r * S(r, Rc1, Rc2) + F_r = U_r * S(r, Rc1, Rc2, True) + F_r * S(r, Rc1, Rc2, False) + print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/system.lt new file mode 100644 index 0000000000..98213116d8 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/system.lt @@ -0,0 +1,192 @@ +# Description: +# +# This example shows how to build a multicomponent spherical vesicle. +# The lipid bilayer is composed of two different lipids (DPPC and DLPC), +# The vesicle contains 120 trans-membrane protein inclusions. +# +# The DPPC lipid model is described here: +# G. Brannigan, P.F. Philips, and F.L.H. Brown, +# Physical Review E, Vol 72, 011915 (2005) +# The protein model is described here: +# G. Bellesia, AI Jewett, and J-E Shea, +# Protein Science, Vol19 141-154 (2010) +# The new DLPC model is a truncated version of DPPC, +# (Its behaviour has not been rigorously tested.) +# Note that 50%/50% mixtures of DPPC & DLPC are commonly used to +# build liposomes http://www.ncbi.nlm.nih.gov/pubmed/10620293 +# +# NOTE: THE COORDINATES FOR THESE MOLECULES ARE GENERATED BY PACKMOL (see below) +# +# NOTE: +# This example may require additional features to be added to LAMMPS. +# If LAMMPS complains about an "Invalid pair_style", then copy the code +# in the "additional_lammps_code" directory into your LAMMPS "src" directory +# and recompile LAMMPS. + +# First, load the definitions of the molecules we will need: + +import "CGLipidBr2005.lt" +using namespace CGLipidBr2005 + +import "1beadProtSci2010.lt" +using namespace 1beadProtSci2010 + +# PREREQUISITES: +# Coordinates for the molecules in this example are loaded from an .XYZ file +# created by PACKMOL. This must be done in advance. (See ../packmol_files/) +# +# The XYZ file was created by PACKMOL in 3 steps: +# (Add the proteins, then pack lipids in the inner & outer layers around them.) +# +# step1) Creae 120 proteins. Distribute them on the surface of the sphere. +# +# step2) Keeping the coordinates from step1 fixed, +# a) first we add 9500 DPPC lipids to the inner monolayer +# b) then we add 9500 DLPC lipids to the inner monolayer +# +# step3) Keeping the coordinates from steps 1 and 2 fixed, +# a) first we add 12500 DPPC lipids to the outer monolayer +# b) then we add 12500 DLPC lipids to the outer monolayer +# +# The order that molecules are created in moltemplate should match the order +# they appear in the final XYZ file created by PACKMOL. (See above.) +# Consequently I instantiate the molecules in the same order here: + + +# Step 1) ---- protein inclusions ---- + +proteins = new 4HelixInsideOut [120] + +# Step 2a) ---- inner monolayer ---- +dppc_in = new DPPC [9500] +# Step 2b) +dlpc_in = new DLPC [9500] + +# Step 3a) ---- outer monolayer ---- +dppc_out = new DPPC [12500] +# Step 3b) +dlpc_out = new DLPC [12500] + + + +# ------------------ boundary conditions -------------------- + +write_once("Data Boundary") { + -500.0 500.0 xlo xhi + -500.0 500.0 ylo yhi + -500.0 500.0 zlo zhi +} + + +write_once("In Settings") { + + # ----------------------------------------------------------- + # -------- interactions between protein and lipids ---------- + # ----------------------------------------------------------- + + # Interactions between the protein and lipid atoms are usually + # determined by mixing rules. (However this is not possible some + # for atoms, such as the "int" atoms in the lipid model which + # interact using -1/r^2 attraction.) Mixing rules do not make + # sense for these atoms so we must explicitly define their + # interaction with all other atoms. + + # We want the hydrophobic interactions between hydrophobic residues in + # the protein and beads the interior of the lipid to be energetically + # similar to the attractive interactions between the lipid tails. + # + # Note: I made the width of the outward-facing protein beads slightly larger + # ("12.5") whenever they interact with the "tail" beads in each lipid + # (in order to make the protein wider there). + # This hopefully relieves some of the internal negative pressure in the center + # of the bilayer which can otherwise rip apart the protein or suck it into + # the bilaer. (This is a hack, and I'm not sure if it is necessary. + # For different protein or lipid models, you probably don't need this.) + # + # i j pairstylename eps sig K L + + pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 12.5 0.4 -1 + pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 + + # To help keep the protein from tilting 90 degrees and burying itself + # within the lipid bilayer, we make the turn regions at either + # end of the protein (strongly) attracted to the head groups + # of the lipid. (In reality, they would probably be attracted + # to the water as well.) + + pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 + pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 + + # All other interactions between proteins and lipids are steric. + + pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + + + # ----------------------------------------------------------- + # -------- Modifications to the protein model: -------------- + # ----------------------------------------------------------- + # + # Turn off attraction between the hydrophobic "@atom:sH" beads: + # (These beads are located in the outside of a trans-membrane protein.) + + pair_coeff @atom:1beadProtSci2010/sH @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0 + + # (Why: These beads are only attracted to + # each other in an aqueous environment) + + # ... and + # Turn ON attraction between the hydrophilic "@atom:sL" beads. + # (These beads are located in the interior of a trans-membrane protein.) + + pair_coeff @atom:1beadProtSci2010/sL @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 + + # Why? + # In reality, polar groups in the interior of trans-membrane + # proteins do form hydrogen bonds with each other. This was + # absent from the original protein model because, in an aqueous + # environment, these groups preferentially interact with the water. + # + # Why is this necessary? + # Shouldn't attraction between lipid tails and the protein create + # an effective force which brings the hydrophilic beads together? + # (similar to the hydrophobic effect, but in reverse?). + # Answer: + # Unlike an aqueous environment (~zero pressure, or +1atm), there is + # a large negative pressure in the interior of some bilayer membrane + # models (such as this one). Without some kind of direct attraction + # between interior residues, the protein will get pulled apart. + # (Perhaps the attractive force I am using is too strong?) + +} + + +# Finally, we must combine the two force-field styles which were used for +# the coarse-grained lipid and protein. To do that, we write one last time +# to the "In Init" section. When reading the "Init" section LAMMPS will +# read these commands last and this will override any earlier settings. + +write_once("In Init") { + # -- These styles override earlier settings -- + units real + atom_style full + # (Hybrid force field styles were used for portability.) + bond_style hybrid harmonic + angle_style hybrid cosine/delta harmonic + dihedral_style hybrid fourier + improper_style none + pair_style hybrid table linear 1130 lj/charmm/coul/charmm/inter es4k4l 14.5 15 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" + communicate multi +} + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/table_int.dat b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/table_int.dat new file mode 100644 index 0000000000..b0d651d67f --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/table_int.dat @@ -0,0 +1,1139 @@ +# Table for the INT-INT interaction from +# Brannigan et al, Phys Rev E, 72, 011915 (2005) +# This table contains +# i r_i U(r_i) -dU/dr|r_i +# where U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) + +INT +N 1130 + +1 0.02 2.0331818401e+30 1.21990910406e+33 +2 0.04 4.9638228518e+26 1.48914685554e+29 +3 0.06 3.82579033251e+24 7.65158066501e+26 +4 0.08 1.21187081343e+23 1.81780622014e+25 +5 0.1 8.32791281704e+21 9.99349538045e+23 +6 0.12 9.34030842897e+20 9.34030842897e+22 +7 0.14 1.46892540453e+20 1.25907891817e+22 +8 0.16 2.95866897809e+19 2.21900173357e+21 +9 0.18 7.19889946863e+18 4.79926631242e+20 +10 0.2 2.0331818401e+18 1.21990910406e+20 +11 0.22 6.47834392264e+17 3.53364213962e+19 +12 0.24 2.28034873754e+17 1.14017436877e+19 +13 0.26 8.72681951932e+16 4.02776285507e+18 +14 0.28 3.58624366341e+16 1.53696157003e+18 +15 0.3 1.56704372019e+16 6.26817488078e+17 +16 0.32 7.2233129348e+15 2.70874235055e+17 +17 0.34 3.48970861422e+15 1.23166186384e+17 +18 0.36 1.75754381558e+15 5.85847938527e+16 +19 0.38 9.18613895646e+14 2.90088598625e+16 +20 0.4 4.96382285179e+14 1.48914685554e+16 +21 0.42 2.76404230108e+14 7.89726371739e+15 +22 0.44 1.58162693423e+14 4.31352800247e+15 +23 0.46 9.27773983256e+13 2.42027995633e+15 +24 0.48 5.56725765996e+13 1.391814415e+15 +25 0.5 3.41111308981e+13 8.18667141564e+14 +26 0.52 2.13057117167e+13 4.91670270393e+14 +27 0.54 1.35459994024e+13 3.0102220895e+14 +28 0.56 8.75547769351e+12 1.87617379153e+14 +29 0.58 5.74645813711e+12 1.18892237325e+14 +30 0.6 3.8257903322e+12 7.65158066491e+13 +31 0.62 2.58128463312e+12 4.99603477424e+13 +32 0.64 1.7635041342e+12 3.30657025205e+13 +33 0.66 1.21901470178e+12 2.21639036726e+13 +34 0.68 8.51979641904e+11 1.50349348607e+13 +35 0.7 6.0167184547e+11 1.0314374497e+13 +36 0.72 4.29087845387e+11 7.15146409276e+12 +37 0.74 3.08855637556e+11 5.00846980094e+12 +38 0.76 2.24270970425e+11 3.54112058818e+12 +39 0.78 1.64210505205e+11 2.52631546702e+12 +40 0.8 1.2118708117e+11 1.81780621971e+12 +41 0.82 90109367359.1 1.31867367068e+12 +42 0.84 67481501334.4 9.64021449503e+11 +43 0.86 50880896383.4 7.09965997788e+11 +44 0.88 38613938681.2 5.26553710913e+11 +45 0.9 29486692086.8 3.93155896009e+11 +46 0.92 22650731882.4 2.95444330322e+11 +47 0.94 17498544395.3 2.23385674464e+11 +48 0.96 13591937526.4 1.69899220331e+11 +49 0.98 10612635712.6 1.29950642555e+11 +50 1.0 8327912706.34 99934953582.6 +51 1.02 6566502316.69 77252969474.2 +52 1.04 5201589672.36 60018343356.8 +53 1.06 4138717434.11 46853405843.3 +54 1.08 3307128665.58 36745874940.0 +55 1.1 2653529579.27 28947596241.1 +56 1.12 2137567708.15 22902511945.9 +57 1.14 1728534024.3 18195095739.0 +58 1.16 1402943799.0 14513212422.1 +59 1.18 1142752163.37 11621209113.9 +60 1.2 934030766.093 9340308300.6 +61 1.22 765981286.774 7534242773.65 +62 1.24 630196371.787 6098675145.29 +63 1.26 520103253.414 4953364870.6 +64 1.28 430542934.103 4036340534.04 +65 1.3 357450462.101 3299543229.91 +66 1.32 297610947.802 2705554551.18 +67 1.34 248472587.186 2225128105.44 +68 1.36 208002782.573 1835319108.76 +69 1.38 174576985.011 1518061159.35 +70 1.4 146892484.084 1259078837.33 +71 1.42 123901294.937 1047053582.16 +72 1.44 104757721.536 872981382.419 +73 1.46 88777241.639 729676313.267 +74 1.48 75404158.02 611385405.387 +75 1.5 64186061.7033 513488820.507 +76 1.52 54753607.1486 432265633.695 +77 1.54 46804443.7318 364710253.134 +78 1.56 40090410.0598 308388060.159 +79 1.58 34407297.9713 261321529.95 +80 1.6 29586646.6744 221900119.2 +81 1.62 25489145.661 188808745.634 +82 1.64 21999316.2868 160970856.824 +83 1.66 19021212.5921 137502982.517 +84 1.68 16474936.8715 117678352.86 +85 1.7 14293808.3245 100897694.735 +86 1.72 12422056.6082 86665727.6626 +87 1.74 10812938.3788 74572197.8496 +88 1.76 9427195.57103 64276535.39 +89 1.78 8231790.46096 55495411.7777 +90 1.8 7198865.45512 47992625.088 +91 1.82 6304885.77339 41570857.9644 +92 1.84 5529931.32911 36064946.1544 +93 1.86 4857110.59557 31336368.341 +94 1.88 4272074.43377 27268725.7382 +95 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0.000000 15.000000 + 3 0.000000 0.000000 7.500000 diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/DPPC.xyz b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/DPPC.xyz new file mode 100644 index 0000000000..c25a2dbd1a --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/DPPC.xyz @@ -0,0 +1,7 @@ +5 + DPPC coarse-grained lipid + 1 0.000000 0.000000 33.750000 + 2 0.000000 0.000000 26.250000 + 3 0.000000 0.000000 18.750000 + 3 0.000000 0.000000 11.250000 + 3 0.000000 0.000000 3.750000 diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/README.sh b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/README.sh new file mode 100644 index 0000000000..daf17fa827 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/README.sh @@ -0,0 +1,20 @@ +# Here we generate the starting coordinates of the simulation +# using PACKMOL + +# You must run each packmol commend one after the other +# NOTE: If PACKMOL gets stuck in an endless loop, then edit the corresponding +# "inp" file. This should not happen. You can also usually interrupt +# packmol after 30 minutes, and the solution at that point should be good +# enough for use. +packmol < step1_proteins.inp # This step determines the protein's location + # It takes ~20 minutes (on an intel i7) +packmol < step2_innerlayer.inp # this step builds the inner monolayer + # It takes ~90 minutes +packmol < step3_outerlayer.inp # this step builds the outer monolayer + # It takes ~4 hours + +# Running these three commands will probably take about an hour. +# (It depends on how uniformly you need the packing to be.) + +mv -f step3_outerlayer.xyz ../system.xyz + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/protein.xyz b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/protein.xyz new file mode 100644 index 0000000000..75557e6ffb --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/protein.xyz @@ -0,0 +1,75 @@ +73 + +6 -2.11383 -5.225 -29.7 +6 -5.225 -2.11383 -26.4 +7 -8.33617 -5.225 -23.1 +7 -5.225 -8.33617 -19.8 +6 -2.11383 -5.225 -16.5 +6 -5.225 -2.11383 -13.2 +7 -8.33617 -5.225 -9.9 +7 -5.225 -8.33617 -6.6 +6 -2.11383 -5.225 -3.3 +6 -5.225 -2.11383 0 +7 -8.33617 -5.225 3.3 +7 -5.225 -8.33617 6.6 +6 -2.11383 -5.225 9.9 +6 -5.225 -2.11383 13.2 +7 -8.33617 -5.225 16.5 +7 -5.225 -8.33617 19.8 +6 5.225 -2.11383 -26.4 +6 2.11383 -5.225 -23.1 +7 5.225 -8.33617 -19.8 +7 8.33617 -5.225 -16.5 +6 5.225 -2.11383 -13.2 +6 2.11383 -5.225 -9.9 +7 5.225 -8.33617 -6.6 +7 8.33617 -5.225 -3.3 +6 5.225 -2.11383 0 +6 2.11383 -5.225 3.3 +7 5.225 -8.33617 6.6 +7 8.33617 -5.225 9.9 +6 5.225 -2.11383 13.2 +6 2.11383 -5.225 16.5 +7 5.225 -8.33617 19.8 +7 8.33617 -5.225 23.1 +6 2.11383 5.225 -23.1 +6 5.225 2.11383 -19.8 +7 8.33617 5.225 -16.5 +7 5.225 8.33617 -13.2 +6 2.11383 5.225 -9.9 +6 5.225 2.11383 -6.6 +7 8.33617 5.225 -3.3 +7 5.225 8.33617 0 +6 2.11383 5.225 3.3 +6 5.225 2.11383 6.6 +7 8.33617 5.225 9.9 +7 5.225 8.33617 13.2 +6 2.11383 5.225 16.5 +6 5.225 2.11383 19.8 +7 8.33617 5.225 23.1 +7 5.225 8.33617 26.4 +6 -5.225 2.11383 -19.8 +6 -2.11383 5.225 -16.5 +7 -5.225 8.33617 -13.2 +7 -8.33617 5.225 -9.9 +6 -5.225 2.11383 -6.6 +6 -2.11383 5.225 -3.3 +7 -5.225 8.33617 0 +7 -8.33617 5.225 3.3 +6 -5.225 2.11383 6.6 +6 -2.11383 5.225 9.9 +7 -5.225 8.33617 13.2 +7 -8.33617 5.225 16.5 +6 -5.225 2.11383 19.8 +6 -2.11383 5.225 23.1 +7 -5.225 8.33617 26.4 +7 -8.33617 5.225 29.7 +8 -3.35683 -4.56775 24.0698 +8 0.795667 -6.90708 26.8152 +8 4.78683 -3.13225 27.0802 +8 2.75642 6.08575 -28.7448 +8 6.54133 3.72717 -31.9651 +8 5.58525 -1.68575 -31.7552 +8 3.35683 4.56775 29.8448 +8 -0.795667 6.90708 32.5903 +8 -4.78683 3.13225 32.8552 diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/step1_proteins.inp b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/step1_proteins.inp new file mode 100644 index 0000000000..abb48db7d6 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/step1_proteins.inp @@ -0,0 +1,49 @@ +# Step 1: Create a sphere of proteins lying +# (In step 2 we will pack lipids around these proteins +# +# ----- Run using: ----- +# packmol < step1_proteins.inp +# (This takes about 30 minutes on an Intel i7 processor) + + +# ----- Settings: ----- + +# All the atoms from diferent proteins will be at least 50.0 Angstrons apart. +tolerance 50.0 +# (Setting "discale" to 2.0 increases the typical separation +# distance to approximately 2.0*50.0 = 100.0 Angstroms.) +discale 2.0 +# The other parameters below are optional: +nloop 10000 +maxit 20 +seed 12345 +sidemax 3000.0 +# What fraction of the molecules are moved during "large moves"? (default 0.05) +movefrac 0.05 + + +# The output file name + +output step1_proteins.xyz + + +# File types are in xyz format + +filetype xyz + + + +# First, specify the protein inclusions +# We will pack the lipids around these later + +structure protein.xyz + number 120 + atoms 68 69 70 + inside sphere 0. 0. 0. 273.75 + end atoms + atoms 65 66 67 71 72 73 + outside sphere 0. 0. 0. 325.0 + end atoms +end structure + + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/step2_innerlayer.inp b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/step2_innerlayer.inp new file mode 100644 index 0000000000..9f61960f2e --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/step2_innerlayer.inp @@ -0,0 +1,70 @@ +# NOTE: YOU MUST COMPLETE STEP 1 BEFORE RUNNING PACKMOL ON THIS FILE + +# Step 2: Pack the lipids in the inner monolayer around the proteins from step1. +# +# ----- Run using: ----- +# packmol < step2_innerlayer.inp +# (This takes about 90 minutes on an Intel i7 processor) + + +# ----- Settings: ----- + +# All the atoms from diferent molecules will be at least 5.5 Angstrons apart +tolerance 5.5 +# (Setting "discale" to 1.4 increases the typical separation +# distance to approximately 1.4*5.5 = 7.7 Angstroms.) +discale 1.4 +# The other parameters below are optional: +nloop 10000 +maxit 20 +seed 12345 +sidemax 3000.0 +# What fraction of the molecules are moved during "large moves"? (default 0.05) +movefrac 0.05 + + +# The output file name + +output step2_innerlayer.xyz + +# File types are in xyz format + +filetype xyz + + +# The proteins whose position we determined earlier in step 1 +# will be frozen in place during this step. + +structure step1_proteins.xyz + number 1 + fixed 0. 0. 0. 0. 0. 0. +end structure + + +# 9500 DPPC lipids will be put in a shell with their hydrophilic heads +# (atom 1) pointing inwards, and their tails (atom 5) pointing outwards. + + +structure DPPC.xyz + number 9500 + atoms 1 + inside sphere 0. 0. 0. 270.0 + end atoms + atoms 5 + outside sphere 0. 0. 0. 295.0 + end atoms +end structure + +# 9500 DLPC lipids will be put in a shell with their hydrophilic heads +# (atom 1) pointing inwards, and their tails (atom 4) pointing outwards. + +structure DLPC.xyz + number 9500 + atoms 1 + inside sphere 0. 0. 0. 273.0 + end atoms + atoms 4 + outside sphere 0. 0. 0. 295.0 + end atoms +end structure + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/step3_outerlayer.inp b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/step3_outerlayer.inp new file mode 100644 index 0000000000..bed1c04246 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/step3_outerlayer.inp @@ -0,0 +1,70 @@ +# NOTE: YOU MUST COMPLETE STEPS 1 AND 2 BEFORE RUNNING PACKMOL ON THIS FILE + +# Step 3: Pack the lipids in the outer monolayer around the proteins from step1. +# +# ----- Run using: ----- +# packmol < step3_outerlayer.inp +# (This takes about 4 hours on an Intel i7 processor) + + +# ----- Settings: ----- + +# All the atoms from diferent molecules will be at least 5.5 Angstrons apart +tolerance 5.5 +# (Setting "discale" to 1.4 increases the typical separation +# distance to approximately 1.4*5.5 = 7.7 Angstroms.) +discale 1.4 +# The other parameters below are optional: +nloop 10000 +maxit 20 +seed 12345 +sidemax 3000.0 +# What fraction of the molecules are moved during "large moves"? (default 0.05) +movefrac 0.05 + + +# The output file name + +output step3_outerlayer.xyz + +# File types are in xyz format + +filetype xyz + + +# The proteins and lipids whose position we determined earlier in steps 1-2 +# will be frozen in place during this step. + +structure step2_innerlayer.xyz + number 1 + fixed 0. 0. 0. 0. 0. 0. +end structure + + +# 12500 DPPC lipids will be put in a shell with their hydrophilic heads +# (atom 1) pointing outwards, and their tails (atom 5) pointing inwards. + + +structure DPPC.xyz + number 12500 + atoms 5 + inside sphere 0. 0. 0. 310.0 + end atoms + atoms 1 + outside sphere 0. 0. 0. 336.0 + end atoms +end structure + +# 12500 DLPC lipids will be put in a shell with their hydrophilic heads +# (atom 1) pointing outwards, and their tails (atom 4) pointing inwards. + +structure DLPC.xyz + number 12500 + atoms 4 + inside sphere 0. 0. 0. 313.0 + end atoms + atoms 1 + outside sphere 0. 0. 0. 332.0 + end atoms +end structure + diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/run.in.min b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/run.in.min new file mode 100644 index 0000000000..cb374fea13 --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/run.in.min @@ -0,0 +1,58 @@ +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# So, after typing "make yes-user-misc" in to the shell, ... +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. +# +# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style" +# then you made a mistake in the instructions above. + + + +# -- Init section -- + +include system.in.init + +# -- Atom definition section -- + +read_data system.data + +# Read in the coordinates generated by packmol: +# (This takes a while, unfortunately.) + +include system.in.coords + +# If you repeat minimization later, you can skip the (slow) step above which +# reads the coordinaes, by commenting it out and uncommenting this line below: +# +# read_restart system_t0.rst + +# -- Settings Section -- + +include system.in.settings + +# -- Run section -- + +write_restart system_t0.rst + +dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz + +# minimize + +minimize 1.0e-5 1.0e-7 5000 20000 + +# If minimization crashes, then instead try Langevin dynamics +# with a small timestep and a fast damping parameter. For example: +# +# timestep 0.05 +# fix fxlan all langevin 300.0 300.0 100.0 48279 +# fix fxnve all nve +# +# run 10000 + +write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/run.in.nvt new file mode 100644 index 0000000000..3cb0e7067a --- /dev/null +++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/run.in.nvt @@ -0,0 +1,70 @@ +# -------- REQUIREMENTS: --------- +# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +# 2) It also may require additional features and bug fixes for LAMMPS. +# So, after typing "make yes-user-misc" in to the shell, ... +# be sure to download and copy the "additional_lammps_code" from +# http://moltemplate.org (upper-left corner menu) +# 3) Unpack it +# 4) copy the .cpp and .h files to the src folding of your lammps installation. +# 5) Compile LAMMPS. +# +# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style" +# then you made a mistake in the instructions above. +# +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +# Commenting out: +# +# read_data system.data +# +# Instead read the restart file created by "run.in.min". + +read_restart system_after_min.rst + +# WARNING: Unfortunately the LAMMPS "read_restart" command has been undependable +# over the past year (2012). If this fails, then just move the minimization +# steps in run.in.min into this script (into the "Run Section"). +# Alternately, try to extract the last frame of the dump file created +# by run.in.min using "read_dump", "dump2data.py", and/or "restart2data". + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + +# Just in case the previous minimization failed, try again. +# (I don't know why this would help, but sometimes loading +# up the restart file and trying again does help. Magic.) + +minimize 1.0e-5 1.0e-7 5000 20000 + +# Run main simulation + +timestep 10.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs +dump 1 all custom 2500 traj_nvt.lammpstrj id mol type x y z ix iy iz + + +thermo_style custom step temp pe etotal vol epair ebond eangle +thermo 100 # time interval for printing out "thermo" data + + + + +fix fxlan all langevin 300.0 300.0 120 48279 +fix fxnve all nve + +# Note: The energy scale "epsilon" = 2.75kJ/mole = 330.7485200981 Kelvin*kB. +# So a temperature of 300.0 Kelvin corresponds to 0.907033536873*epsilon. +# Note: The langevin damping parameter "120" corresponds to +# the 0.12ps damping time used in Watson et. al JCP 2011. + +run 1000000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README.TXT b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README.TXT new file mode 100644 index 0000000000..c3173a1e19 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README.TXT @@ -0,0 +1,17 @@ + +This directory contains an example of a couarse-grained (vaguely protein-like) +heteropolymer consisting of 14 residues, each of which has 2 atoms +(one backbone atom, one residue atom.) + +There are two types of residues, H and P. +The R-atom for the H residue are attracted to eachother. +All other atoms are repulsive. + +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_run.sh b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_run.sh new file mode 100755 index 0000000000..1347aebbb4 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_run.sh @@ -0,0 +1,20 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The "run.in.nvt" file is a LAMMPS input script containing +# references to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.nvt + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_setup.sh b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_setup.sh new file mode 100755 index 0000000000..acc5fbbaad --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_setup.sh @@ -0,0 +1,23 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_visualize.txt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_visualize.txt new file mode 100644 index 0000000000..5d97ea56ad --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_visualize.txt @@ -0,0 +1,86 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=0.jpg b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=0.jpg new file mode 100644 index 0000000000..a57d0309c3 Binary files /dev/null and b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=0.jpg differ diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=1000ps.jpg b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=1000ps.jpg new file mode 100644 index 0000000000..c77d7ee9d9 Binary files /dev/null and b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=1000ps.jpg differ diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 0000000000..a30fdf733f --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,1728 @@ +PSF + + 1 !NTITLE + REMARKS VMD generated structure x-plor psf file + + 756 !NATOM + 1 1 1 1 0.000000 13.0000 0 + 2 1 3 3 0.000000 50.0000 0 + 3 1 1 1 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b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead.lt new file mode 100644 index 0000000000..eb1820ec7b --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead.lt @@ -0,0 +1,173 @@ +# In this example, we define two types of molecules: "H" and "P", +# both containing two atoms, named "CA" and "R". +# +# @R +# | +# @CA +# +# Eventually, we will connect multiple "H" and "P" molecules +# together to form a polymer, as shown below: +# +# @R @R +# | | +# _@CA_ _@CA_ +# ... -.@CA-' `-@CA-' ` ... +# | | +# @R @R +# +# Suppose that the "H" and "P" molecules both use the same +# type of backbone atom ("CA"), but have their own custom "R" +# sidechain atoms with different properties: +# The "R" atoms belonging to "H" molecules are attracted to each other. +# The "R" atoms in "P" molecules are not. +# +# (Note: There is no reason the "H" and "P" molecules in this example need +# to contain the same number of atoms, or the same atom names. +# The point of this example is to illustrate how to share atom types +# and also the difference between local and global atom types.) +# +# By default, all counter variables are local. This means that whenever +# an atom type (or other counter variable) appears inside a molecule +# definition using the normal syntax "@atom:R", that atom type is a local +# property of the the "H" or "P" molecule in which it appears. +# Any properties assigned to the "R" atoms in either molecule are unique +# to that molecule. +# +# However in order to share "CA" atom types, we will override this behavior +# using the "@atom:../CA" syntax instead of "@atom:CA". This will define +# the "CA" atom in the outer (global) environment, and any properties +# (mass, radius, etc...) assigned to the "@atom:../CA" atom apply to +# "CA" atoms in both the the "H" and "P" molecules (and everywhere else). +# +# This might not be a desirable. "CA" is a popular name for carbon +# atoms in different types of molecules. We don't want to prevent other +# molecules from using this atom name. So we enclose the "CA" atom, +# (along with the definitions of the "H" and "P" molecules) within a +# namespace/environment object ("2bead"). This makes the definition +# of "H" and "P" more portable. Later on we can combine "H" and "P" +# molecules with other molecules without worrying whether they contain +# "CA" atoms with different properties. +# +# Note: In this example "2bead" is NOT a molecule. (Because it contains no +# "write("Data Atoms")" section of its own.) "2bead" is simply the +# name of an environment in which other molecules (H,P) are defined. + + + + +2bead { + + # LAMMPS supports a large number of force-field styles. We must select + # which ones we need. This information belongs in the "In Init" section. + # (Hybrid styles used for portability. These choices can be overridden later.) + + write_once("In Init") { + # -- Default styles for "2bead" -- + units real + atom_style full + # (Hybrid force fields were not necessary but are used for portability.) + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid charmm + pair_style hybrid lj/cut 11.0 + + # If charges are needed, (assuming biopolymers), try one of: + #dielectric 80.0 + #pair_style hybrid lj/cut/coul/debye 0.1 11.0 + # or (for short distances, below a couple nm) + #pair_style hybrid lj/charmm/coul/charmm/implicit 9.0 11.0 + + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 0.0 + } + + + # Define H (the "hydrophobic" residue) + H { + # atom-id mol-id atom-type charge x y z + write("Data Atoms") { + $atom:CA $mol:... @atom:../CA 0.0 0.000 1.0000 0.0000000 + $atom:R $mol:... @atom:R 0.0 0.000 4.4000 0.0000000 + } + write("Data Bonds") { + $bond:CR @bond:../sidechain $atom:CA $atom:R + } + } + + + # Define P (the "polar" residue) + P { + # atom-id mol-id atom-type charge x y z + write("Data Atoms") { + $atom:CA $mol:... @atom:../CA 0.0 0.000 1.0000 0.0000000 + $atom:R $mol:... @atom:R 0.0 0.000 4.4000 0.0000000 + } + write("Data Bonds") { + $bond:CR @bond:../sidechain $atom:CA $atom:R + } + } + + # (Note: Again, atom types, bond-types, (dihedral-types, any variable, etc) + # can be shared. The ".." in "@atom:../CA" tells moltemplate that + # atom type CA is defined in the parent's environment. (We are + # sharing the CA atom type between both the H and P residues. + # The same is true of the ".." in "@bond:../sidechain". + # + # + # Note: The "..." in "$mol:..." tells moltemplate that this molecule may + # be a part of a larger molecule, and (if so) to use the larger + # molecule's id number as it's own. + + + + # There are 3 atom types: the R sidechain (belonging to the H and P residues) + # and the CA sidechain atom (shared by both residues) + + write_once("Data Masses") { + @atom:CA 13.0 + @atom:H/R 50.0 + @atom:P/R 50.0 + } + + + # -------------------------------------------------------------------- + # -- In this example, all force field parameters are stored in the -- + # -- file named "In Settings". They can also go in sections like -- + # -- "Data Pair Coeffs", "Data Bond Coeffs", "Data Angle Coeffs"... -- + # -------------------------------------------------------------------- + + + # 2-body (non-bonded) interactions: + # + # Uij(r) = 4*eps_ij * ( (sig_ij/r)^12 - (sig_ij/r)^6 ) + # + # Hydrophobic side-chains are attractive (large epsilon parameter). + # Polar side-chains and backbone atoms are not attractive (small epsilon). + # + # i j pairstylename eps sig + # + write_once("In Settings") { + pair_coeff @atom:CA @atom:CA lj/cut 0.10 2.0 + pair_coeff @atom:H/R @atom:H/R lj/cut 2.50 3.6 + pair_coeff @atom:P/R @atom:P/R lj/cut 0.10 3.6 + } + # + # (Interactions between different atom types use "arithmetic" mixing rules.) + + + # 2-body (bonded) interactions: + # + # Ubond(r) = (k/2)*(r-0)^2 + # + # The corresponding command is: + # + # bond_coeff bondType bondstylename k r0 + # + + write_once("In Settings") { + bond_coeff @bond:sidechain harmonic 30.0 3.4 + bond_coeff @bond:backbone harmonic 30.0 3.7 + } + +} # 2bead + diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead_angles.lt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead_angles.lt new file mode 100644 index 0000000000..c378609ac3 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead_angles.lt @@ -0,0 +1,61 @@ +# Although there's no need to define angular interactions (because the "H" +# and "P" molecules only contains two atoms), we define the settings for angles +# or dihedrals which might be present later when we connect multiple "H" and "P" +# molecules together to build a polymer. + +2bead { + + # OPTIONAL: Enclose these angle settings within the 2bead {...} environment. + # We do this for the same reason we enclosed "H" and "P" in "2bead". + # This does not overwrite the definition of 2bead. Here we are only + # augmenting "2bead" to include definitions of the following angles + + # Rules for determining 3 and 4-body bonded interactions by type + + # angle-type atomType1 atomType2 atomType3 bondType1 bondType2 + + write_once("Data Angles By Type") { + @angle:backbone @atom:CA @atom:CA @atom:CA @bond:* @bond:* + @angle:sidechain @atom:CA @atom:CA @atom:*/R @bond:* @bond:* + } + + # dihedral-type AtomType1 AtomType2 AtomType3 AtomType4 bondType1 btyp2 btyp3 + + write_once("Data Dihedrals By Type") { + @dihedral:CCCC @atom:CA @atom:CA @atom:CA @atom:CA @bond:* @bond:* @bond:* + @dihedral:RCCR @atom:*/R @atom:CA @atom:CA @atom:*/R @bond:* @bond:* @bond:* + } + + # 3-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Uangle(theta) = (k/2)*(theta-theta0)^2 + # (k in kcal/mol/rad^2, theta0 in degrees) + # + # The corresponding command is: + # + # angle_coeff angleType anglestylename k theta0 + + write_once("In Settings") { + angle_coeff @angle:backbone harmonic 30.00 114 + angle_coeff @angle:sidechain harmonic 30.00 123 + } + + + # 4-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Udihedral(phi) = K * (1 + cos(n*phi - d)) + # + # The d parameter is in degrees, K is in kcal/mol/rad^2. + # + # The corresponding command is + # dihedral_coeff dihedralType dihedralstylename K n d w + # "w" is the weight for 1-4 pair interactions, which we set to 0.0 + + write_once("In Settings") { + dihedral_coeff @dihedral:CCCC charmm -0.5 1 -180 0.0 + dihedral_coeff @dihedral:RCCR charmm -1.5 1 -180 0.0 + } # write_once("In Settings") + +} \ No newline at end of file diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/README.sh b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/README.sh new file mode 100755 index 0000000000..7604a672c6 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/README.sh @@ -0,0 +1,20 @@ +# The version of "2bead.lt" in this directory is defines two types of +# molecules (named "2bead/H" and "2bead/P"). +# +# However, there is another version of this file which is easier to understand. +# I recommend reading that file first. +# It is located at "simplified_version_one_residue/2bead.lt". +# It defines only one type of molecule (named "2bead") +# It is much simpler. + +# ------ + +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + +# run moltemplate + +moltemplate.sh system.lt + +# This will generate various files with names ending in *.in* and *.data. + diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/peptide.lt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/peptide.lt new file mode 100644 index 0000000000..6c70892444 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/peptide.lt @@ -0,0 +1,51 @@ +import "2bead.lt" +import "2bead_angles.lt" + +Peptide { + + # A polymer of alternating "H" and "P" beads: + + res1 = new 2bead/P + res2 = new 2bead/P.rot(180.0, 1,0,0).move(3.2,0,0) + res3 = new 2bead/H.rot( 0.0, 1,0,0).move(6.4,0,0) + res4 = new 2bead/H.rot(180.0, 1,0,0).move(9.6,0,0) + res5 = new 2bead/H.rot( 0.0, 1,0,0).move(12.8,0,0) + res6 = new 2bead/H.rot(180.0, 1,0,0).move(16.0,0,0) + res7 = new 2bead/P.rot( 0.0, 1,0,0).move(19.2,0,0) + res8 = new 2bead/P.rot(180.0, 1,0,0).move(22.4,0,0) + res9 = new 2bead/P.rot( 0.0, 1,0,0).move(25.6,0,0) + res10 = new 2bead/H.rot(180.0, 1,0,0).move(28.8,0,0) + res11 = new 2bead/H.rot( 0.0, 1,0,0).move(32.0,0,0) + res12 = new 2bead/H.rot(180.0, 1,0,0).move(35.2,0,0) + res13 = new 2bead/P.rot( 0.0, 1,0,0).move(38.4,0,0) + res14 = new 2bead/P.rot(180.0, 1,0,0).move(41.6,0,0) + + # Now, link the residues together this way: + write("Data Bonds") { + $bond:backbone1 @bond:2bead/backbone $atom:res1/CA $atom:res2/CA + $bond:backbone2 @bond:2bead/backbone $atom:res2/CA $atom:res3/CA + $bond:backbone3 @bond:2bead/backbone $atom:res3/CA $atom:res4/CA + $bond:backbone4 @bond:2bead/backbone $atom:res4/CA $atom:res5/CA + $bond:backbone5 @bond:2bead/backbone $atom:res5/CA $atom:res6/CA + $bond:backbone6 @bond:2bead/backbone $atom:res6/CA $atom:res7/CA + $bond:backbone7 @bond:2bead/backbone $atom:res7/CA $atom:res8/CA + $bond:backbone8 @bond:2bead/backbone $atom:res8/CA $atom:res9/CA + $bond:backbone9 @bond:2bead/backbone $atom:res9/CA $atom:res10/CA + $bond:backbone10 @bond:2bead/backbone $atom:res10/CA $atom:res11/CA + $bond:backbone11 @bond:2bead/backbone $atom:res11/CA $atom:res12/CA + $bond:backbone12 @bond:2bead/backbone $atom:res12/CA $atom:res13/CA + $bond:backbone13 @bond:2bead/backbone $atom:res13/CA $atom:res14/CA + } + + create_var { $mol } # <--create a molecule ID number for this peptide + + # This causes res1,res2,res3,...,res14 to share the same molecule counter + # because in the 2bead.lt file, the "..." in "$mol:..." preferentially looks + # for a counter of that type in a parent molecule or earlier ancestor. + +} # Peptide + + + +# Angle, dihedral and improper interactions will be generated +# according to the instructions in "2bead_angles.lt" diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/simplified_version_one_residue/2bead_simple.lt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/simplified_version_one_residue/2bead_simple.lt new file mode 100644 index 0000000000..eea38da04a --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/simplified_version_one_residue/2bead_simple.lt @@ -0,0 +1,122 @@ +# This file contains the definition of "2-bead", a simple molecule +# containing two atoms: +# +# @R +# | +# @CA +# +# +# Later on, we may connect them together to form a polymer: +# +# +# @R @R +# | | +# _@CA_ _@CA_ +# ... -.@CA-' `-@CA-' ` ... +# | | +# @R @R +# +# THERE ARE TWO VERSIONS OF THIS FILE: +# In the simple version, shown here, there is only one type of side-chain "R". +# More complex examples have multiple types of molecules +# each with different side-chain properties. + +2bead { + + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:CA $mol:... @atom:CA 0.0 0.000 0.0000 0.0000000 + $atom:R $mol:... @atom:R 0.0 0.000 3.4000 0.0000000 + } + + write_once("Data Masses") { + @atom:C 14.0 + @atom:R 50.0 + } + + write("Data Bonds") { + $bond:CR @bond:sidechain $atom:CA $atom:R + } + + write_once("Data Angles By Type") { + @angle:backbone @atom:CA @atom:CA @atom:CA @bond:* @bond:* + @angle:sidechain @atom:CA @atom:CA @atom:R @bond:* @bond:* + } + + write_once("Data Dihedrals By Type") { + @dihedral:CCCC @atom:CA @atom:CA @atom:CA @atom:CA @bond:* @bond:* @bond:* + @dihedral:RCCR @atom:R @atom:CA @atom:CA @atom:R @bond:* @bond:* @bond:* + } + + + write_once("In Settings") { + # 2-body (bonded) interaction parameters are listed by bondType: + # + # Ubond(r) = (k/2)*(r-0)^2 + # + # The corresponding command is: + # + # bond_coeff bondType harmonic k r0 + # + bond_coeff @bond:sidechain harmonic 30.0 3.4 + bond_coeff @bond:backbone harmonic 30.0 3.7 + + # 3-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Uangle(theta) = (k/2)*(theta-theta0)^2 + # + # The corresponding command is: + # + # angle_coeff angleType harmonic k theta0 + # (The theta0 parameter is in degrees, k is in kcal/mol/rad^2) + + angle_coeff @angle:backbone harmonic 30.0 104 + angle_coeff @angle:sidechain harmonic 30.0 127 + + + # 4-body interactions in this example are listed by atomType and bondType + # The atomIDs involved are determined automatically. The forumula used is: + # + # Udihedral(phi) = K * (1 + cos(n*phi - d)) + # + # The corresponding command is + # dihedral_coeff dihedralType charmm K d w + # + # The d parameter is in degrees, K is in kcal/mol/rad^2. + # "w" is the weight for 1-4 pair interactions, which we set to 0.0. + # This should turn off pairwise interactions between 1-4 bonded atoms + # which are also involved in any of the dihedral interactions below: + # + dihedral_coeff @dihedral:CCCC charmm -0.5 1 180 0.0 + dihedral_coeff @dihedral:RCCR charmm -1.5 1 -90 0.0 + + + # 2-body (non-bonded) interactions are listed by atom type: + + # interaction between atoms of the same type: + # epsilon signma + pair_coeff @atom:CA @atom:CA lj/charmm/coul/charmm 0.010 2.0 + pair_coeff @atom:R @atom:R lj/charmm/coul/charmm 2.50 3.6 + # + # interactions between different atom types use arithmetic mixing rules + + } # write_once("In Settings") + + + write_once("In Init") { + # -- Default styles for "2bead" -- + units real + atom_style full + # (Hybrid force field styles were used for portability.) + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid opls + improper_style none + pair_style hybrid lj/charmm/coul/charmm 9.0 11.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 0.0 + } +} # 2bead + diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/system.lt new file mode 100644 index 0000000000..567ec3ae5d --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/system.lt @@ -0,0 +1,25 @@ +import "peptide.lt" + + +# Specify the periodic boundary conditions: +write_once("Data Boundary") { + 0 180.0 xlo xhi + 0 180.0 ylo yhi + 0 180.0 zlo zhi +} + +# Create 27 peptides in a rectangular grid +peptides = new Peptide [3].move(0, 0, 60.0) + [3].move(0, 60.0, 0) + [3].move(60.0, 0, 0) + +# Now (for fun) shift some of the peptides +# in the x direction by a distance of 25.0 +# Suppose we want to move the middle slice +# (which has constant Z). We do that this way: +peptides[1][*][*].move(25,0,0) +# more examples: +peptides[*][1][*].move(0,0,25) +peptides[*][*][1].move(0,25,0) + + diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/run.in.nvt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/run.in.nvt new file mode 100644 index 0000000000..eb864e049e --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/run.in.nvt @@ -0,0 +1,38 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +# I you want to be careful, you can minimize the system first. (Try using +# "run.in.min" and uncomment the read_restart command in this file below.) +# read_restart system_after_min.rst + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 2.0 +dump 1 all custom 2500 traj_nvt.lammpstrj id mol type x y z ix iy iz + +# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". +# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) + +fix fxlan all langevin 300.0 300.0 5000.0 48279 +fix fxnve all nve + + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo 2500 # time interval for printing out "thermo" data + +restart 1000000 restart_nvt + +run 1000000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/README.TXT b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README.TXT new file mode 100644 index 0000000000..1a077178e3 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README.TXT @@ -0,0 +1,36 @@ +This is a very crude attempt to create a polymer melt +consisting of 150 copies of the same polymer. + +THE FORCE FIELD PARAMETERS AND CONFORMATION FOR THIS SYSTEM ARE COMPLETELY WRONG + +The purpose of this example is to demonstrate one way to create a +large number of randomly generated polymers, and to use +an NPT simulation to pack them all into a small box. +(Smaller than their initial outstretched length.) + +Each polymer is a random heteropolymer of length 200 monomers. +This polymer is a polymoer of PVDF and PCTFE monomers +selected randomly in a 1:3 ratio. +Again, this is not a realistic simulation of PVDV or PCTFE polymers, + +Furthermore, even after the simulation is done, the arrangement of the +polymers in the box is not characteristic of a truly random polymer melt. + + +---- A note on size --- + +This is a large system with nearly 200000 atoms. +It takes several minutes to compile this example +and (currently requiring at least 4.0 Gb of memory). +(I'm working on reducing that requirement. -Andrew 2012-9-12) + +----------------------- + +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_run.sh b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_run.sh new file mode 100755 index 0000000000..ac21c4c45e --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_run.sh @@ -0,0 +1,14 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The "run.in.nvt" file is a LAMMPS input script containing +# references to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.nvt diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_setup.sh b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_setup.sh new file mode 100755 index 0000000000..acc5fbbaad --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_setup.sh @@ -0,0 +1,23 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_visualize.txt b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/2bead.jpg b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/2bead.jpg new file mode 100644 index 0000000000..f67da797f1 Binary files /dev/null and b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/2bead.jpg differ diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/3bead.jpg b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/3bead.jpg new file mode 100644 index 0000000000..15d7b29676 Binary files /dev/null and b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/3bead.jpg differ diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 0000000000..6915e27391 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,277 @@ +PSF + + 1 !NTITLE + REMARKS VMD generated structure x-plor psf file + + 116 !NATOM + 1 1 3 3 0.000000 12.0000 0 + 2 1 4 4 0.000000 17.0000 0 + 3 1 4 4 0.000000 17.0000 0 + 4 1 3 3 0.000000 12.0000 0 + 5 1 4 4 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63 62 64 72 71 73 75 74 76 + 82 81 83 93 92 94 102 101 103 + 109 108 110 + + 47 !NPHI: dihedrals + 38 40 43 46 69 71 74 77 + 1 4 7 9 40 43 46 48 + 67 69 71 74 71 74 77 79 + 35 38 40 43 30 33 35 38 + 28 30 33 35 33 35 38 40 + 57 60 62 65 55 57 60 62 + 4 7 9 11 7 9 11 13 + 13 16 18 20 24 26 28 30 + 62 65 67 69 65 67 69 71 + 81 84 86 88 86 88 90 92 + 92 95 97 99 95 97 99 101 + 108 111 113 115 16 18 20 22 + 18 20 22 24 20 22 24 26 + 22 24 26 28 84 86 88 90 + 9 11 13 16 11 13 16 18 + 26 28 30 33 46 48 50 53 + 53 55 57 60 48 50 53 55 + 60 62 65 67 77 79 81 84 + 79 81 84 86 88 90 92 95 + 90 92 95 97 97 99 101 104 + 104 106 108 111 99 101 104 106 + 106 108 111 113 43 46 48 50 + 50 53 55 57 74 77 79 81 + 101 104 106 108 + + 0 !NIMPHI: impropers + + + 0 !NDON: donors + + + 0 !NACC: acceptors + + + 0 !NNB + + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 + + 1 0 !NGRP + 0 0 0 + diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=0ps.jpg b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=0ps.jpg new file mode 100644 index 0000000000..cc6822e7b3 Binary files /dev/null and b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=0ps.jpg differ diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=1ns.jpg b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=1ns.jpg new file mode 100644 index 0000000000..efcaa76c06 Binary files /dev/null and b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=1ns.jpg differ diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/monomers.lt b/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/monomers.lt new file mode 100644 index 0000000000..9a90c172ae --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/monomers.lt @@ -0,0 +1,115 @@ + # ---------------------------------------------------------------------- + # -- General comment: -- + # -- The write() and write_once() commands create and append text to -- + # -- files (replacing variables beginning with @ or $ with counters.) -- + # -- File names beginning with "In " or "Data " are special. -- + # -- They will be pasted into the LAMMPS input script and -- + # -- data files which are generated by moltemplate. The syntax -- + # -- of these files is exactly the same as the syntax from the -- + # -- corresponding sections of a LAMMPS input script or data file. -- + # ---------------------------------------------------------------------- + + +MonomerTypes { + + + 2bead { + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:CA $mol:... @atom:CA 0.0 0.000 1.000 0.0000 + $atom:R $mol:... @atom:R 0.0 0.000 4.400 0.0000 + } + + # bond-id bond-type atom-id1 atom-id2 + + write("Data Bonds") { + $bond:CR @bond:../sidechain $atom:CA $atom:R + } + + # atom-type mass + + write_once("Data Masses") { + @atom:CA 12.0 + @atom:R 17.0 + } + + # atom-type atom-type epsilon sigma + + write_once("In Settings") { + pair_coeff @atom:CA @atom:CA 0.10 2.0 + pair_coeff @atom:R @atom:R 0.50 3.0 + } + + } # 2bead + + + 3bead { + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:CA $mol:... @atom:CA 0.0 0.000 1.000 0.000 + $atom:R1 $mol:... @atom:R 0.0 0.000 2.700 2.950 + $atom:R2 $mol:... @atom:R 0.0 0.000 2.700 -2.950 + } + + # bond-id bond-type atom-id1 atom-id2 + + write("Data Bonds") { + $bond:CR1 @bond:../sidechain $atom:CA $atom:R1 + $bond:CR2 @bond:../sidechain $atom:CA $atom:R2 + } + + # atom-type mass + + write_once("Data Masses") { + @atom:CA 12.0 + @atom:R 17.0 + } + + # atom-type atom-type epsilon sigma + + write_once("In Settings") { + pair_coeff @atom:CA @atom:CA 0.10 2.0 + pair_coeff @atom:R @atom:R 0.50 3.0 + } + } # 3bead + + + write_once("In Settings") { + # bond-type k r0 + bond_coeff @bond:sidechain 20.0 3.4 + bond_coeff @bond:bb 20.0 3.4 # "bb" shorthand for "backbone" + } + + # Although there's no need to define angular interactions (because this + # "molecule" only contains two atoms), we define the settings for angles + # or dihedrals which might be present later when we build a polymer. + + write_once("In Settings") { + # angle-type k theta0 + angle_coeff @angle:backbone 10.00 160 + angle_coeff @angle:sidechain 10.00 120 + angle_coeff @angle:RCR 10.00 120 + # dihedral-type K1 K2 K3 K4 + dihedral_coeff @dihedral:backbn 0.10 -0.271016 3.145034 0.0 + } + + # Rules for determining 3 and 4-body bonded interactions by type + + # angle-type atomType1 atomType2 atomType3 bondType1 bondType2 + + write_once("Data Angles By Type") { + @angle:backbone @atom:*/CA @atom:*/CA @atom:*/CA @bond:* @bond:* + @angle:sidechain @atom:*/CA @atom:*/CA @atom:*/R @bond:* @bond:* + @angle:RCR @atom:*/R @atom:*/CA @atom:*/R @bond:* @bond:* + } + + # dihedral-type AtomType1 AtomType2 AtomType3 AtomType4 bondType1 btyp2 btyp3 + + write_once("Data Dihedrals By Type") { + @dihedral:backbn @atom:*/CA @atom:*/CA @atom:*/CA @atom:*/CA * * * + } + +} # MonomerTypes + diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/polymer.lt b/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/polymer.lt new file mode 100644 index 0000000000..9497dcc390 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/polymer.lt @@ -0,0 +1,82 @@ +import "monomers.lt" + +using namespace MonomerTypes + +RandomHeteropolymer { + + # Make a chain of monomers with random composition: + + monomers = new random([2bead,3bead], + [0.6,0.4], + 123456) # <-- optional random seed + [50].rot(180,1,0,0).move(2.95, 0, 0) + + # Now, link the monomers together this way: + + write("Data Bonds") { + $bond:bb1 @bond:MonomerTypes/bb $atom:monomers[0]/CA $atom:monomers[1]/CA + $bond:bb2 @bond:MonomerTypes/bb $atom:monomers[1]/CA $atom:monomers[2]/CA + $bond:bb3 @bond:MonomerTypes/bb $atom:monomers[2]/CA $atom:monomers[3]/CA + $bond:bb4 @bond:MonomerTypes/bb $atom:monomers[3]/CA $atom:monomers[4]/CA + $bond:bb5 @bond:MonomerTypes/bb $atom:monomers[4]/CA $atom:monomers[5]/CA + $bond:bb6 @bond:MonomerTypes/bb $atom:monomers[5]/CA $atom:monomers[6]/CA + $bond:bb7 @bond:MonomerTypes/bb $atom:monomers[6]/CA $atom:monomers[7]/CA + $bond:bb8 @bond:MonomerTypes/bb $atom:monomers[7]/CA $atom:monomers[8]/CA + $bond:bb9 @bond:MonomerTypes/bb $atom:monomers[8]/CA $atom:monomers[9]/CA + $bond:bb10 @bond:MonomerTypes/bb $atom:monomers[9]/CA $atom:monomers[10]/CA + $bond:bb11 @bond:MonomerTypes/bb $atom:monomers[10]/CA $atom:monomers[11]/CA + $bond:bb12 @bond:MonomerTypes/bb $atom:monomers[11]/CA $atom:monomers[12]/CA + $bond:bb13 @bond:MonomerTypes/bb $atom:monomers[12]/CA $atom:monomers[13]/CA + $bond:bb14 @bond:MonomerTypes/bb $atom:monomers[13]/CA $atom:monomers[14]/CA + $bond:bb15 @bond:MonomerTypes/bb $atom:monomers[14]/CA $atom:monomers[15]/CA + $bond:bb16 @bond:MonomerTypes/bb $atom:monomers[15]/CA $atom:monomers[16]/CA + $bond:bb17 @bond:MonomerTypes/bb $atom:monomers[16]/CA $atom:monomers[17]/CA + $bond:bb18 @bond:MonomerTypes/bb $atom:monomers[17]/CA $atom:monomers[18]/CA + $bond:bb19 @bond:MonomerTypes/bb $atom:monomers[18]/CA $atom:monomers[19]/CA + $bond:bb20 @bond:MonomerTypes/bb $atom:monomers[19]/CA $atom:monomers[20]/CA + $bond:bb21 @bond:MonomerTypes/bb $atom:monomers[20]/CA $atom:monomers[21]/CA + $bond:bb22 @bond:MonomerTypes/bb $atom:monomers[21]/CA $atom:monomers[22]/CA + $bond:bb23 @bond:MonomerTypes/bb $atom:monomers[22]/CA $atom:monomers[23]/CA + $bond:bb24 @bond:MonomerTypes/bb $atom:monomers[23]/CA $atom:monomers[24]/CA + $bond:bb25 @bond:MonomerTypes/bb $atom:monomers[24]/CA $atom:monomers[25]/CA + $bond:bb26 @bond:MonomerTypes/bb $atom:monomers[25]/CA $atom:monomers[26]/CA + $bond:bb27 @bond:MonomerTypes/bb $atom:monomers[26]/CA $atom:monomers[27]/CA + $bond:bb28 @bond:MonomerTypes/bb $atom:monomers[27]/CA $atom:monomers[28]/CA + $bond:bb29 @bond:MonomerTypes/bb $atom:monomers[28]/CA $atom:monomers[29]/CA + $bond:bb30 @bond:MonomerTypes/bb $atom:monomers[29]/CA $atom:monomers[30]/CA + $bond:bb31 @bond:MonomerTypes/bb $atom:monomers[30]/CA $atom:monomers[31]/CA + $bond:bb32 @bond:MonomerTypes/bb $atom:monomers[31]/CA $atom:monomers[32]/CA + $bond:bb33 @bond:MonomerTypes/bb $atom:monomers[32]/CA $atom:monomers[33]/CA + $bond:bb34 @bond:MonomerTypes/bb $atom:monomers[33]/CA $atom:monomers[34]/CA + $bond:bb35 @bond:MonomerTypes/bb $atom:monomers[34]/CA $atom:monomers[35]/CA + $bond:bb36 @bond:MonomerTypes/bb $atom:monomers[35]/CA $atom:monomers[36]/CA + $bond:bb37 @bond:MonomerTypes/bb $atom:monomers[36]/CA $atom:monomers[37]/CA + $bond:bb38 @bond:MonomerTypes/bb $atom:monomers[37]/CA $atom:monomers[38]/CA + $bond:bb39 @bond:MonomerTypes/bb $atom:monomers[38]/CA $atom:monomers[39]/CA + $bond:bb40 @bond:MonomerTypes/bb $atom:monomers[39]/CA $atom:monomers[40]/CA + $bond:bb41 @bond:MonomerTypes/bb $atom:monomers[40]/CA $atom:monomers[41]/CA + $bond:bb42 @bond:MonomerTypes/bb $atom:monomers[41]/CA $atom:monomers[42]/CA + $bond:bb43 @bond:MonomerTypes/bb $atom:monomers[42]/CA $atom:monomers[43]/CA + $bond:bb44 @bond:MonomerTypes/bb $atom:monomers[43]/CA $atom:monomers[44]/CA + $bond:bb45 @bond:MonomerTypes/bb $atom:monomers[44]/CA $atom:monomers[45]/CA + $bond:bb46 @bond:MonomerTypes/bb $atom:monomers[45]/CA $atom:monomers[46]/CA + $bond:bb47 @bond:MonomerTypes/bb $atom:monomers[46]/CA $atom:monomers[47]/CA + $bond:bb48 @bond:MonomerTypes/bb $atom:monomers[47]/CA $atom:monomers[48]/CA + $bond:bb49 @bond:MonomerTypes/bb $atom:monomers[48]/CA $atom:monomers[49]/CA + } + + # These lines of moltemplate script above were generated in python: + # for i in range(0,49): + # print(' $bond:bb'+str(i+1)+' @bond:MonomerTypes/bb $atom:monomers[' + # +str(i)+']/CA $atom:monomers['+str(i+1)+']/CA') + + # Finally, create a molecule ID number for this large polymer object + + create_var { $mol } + +} # RandomHeteropolymer + + + +# Angle, dihedral and improper interactions will be generated +# automatically according to the instructions in "monomers.lt" diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/system.lt new file mode 100644 index 0000000000..11f2d48fad --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/system.lt @@ -0,0 +1,33 @@ +# LAMMPS supports a large number of force-field styles. We must select +# which ones we need. This information belongs in the "In Init" section (and +# (you can specify it anywhere in your LT files, multiple times if you like). +# If different molecules use different force-field styles, you can use hybrid +# styles. (In this example the molecules share the same pair_style.) + +write_once("In Init") { + units real + atom_style full + bond_style harmonic + angle_style harmonic + dihedral_style opls + pair_style lj/cut 9.0 + # If you have charged molecules immersed in a salty implicit + # solvent, you might try something like this this instead: + # pair_style lj/cut/coul/debye 0.1 9.0 + pair_modify mix arithmetic + dielectric 80.0 + special_bonds lj 0.0 0.0 0.0 +} + + +write_once("Data Boundary") { + 0.0 150.0 xlo xhi + 0.0 150.0 ylo yhi + 0.0 150.0 zlo zhi +} + + +import "polymer.lt" + +polymer = new RandomHeteropolymer + diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/run.in.nvt b/tools/moltemplate/examples/CG_misc/random_heteropolymer/run.in.nvt new file mode 100644 index 0000000000..5e08f03cb2 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/random_heteropolymer/run.in.nvt @@ -0,0 +1,29 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + +timestep 2.0 +dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo 1000 # time interval for printing out "thermo" data + +fix fxlan all langevin 300.0 300.0 120 48279 +fix fxnve all nve + +# Temperature = 500 degrees + +run 500000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_misc/translocation/README.TXT b/tools/moltemplate/examples/CG_misc/translocation/README.TXT new file mode 100644 index 0000000000..b9bac96d50 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/README.TXT @@ -0,0 +1,23 @@ + +This example contains a (crude and somewhat simple) example of +the translocation of a (rather short) polymer through a hole in a wall, +surrounded by an explicit LJ solvent. + +(I used a short polymer because a longer polymer would require a larger box. + But this example looked more impressive visually when I used a smaller box.) +---- +Note: You must compile LAMMPS with the optional "RIGID" package installed. To + do this, go to the "src" directory of your lammps installation and type: + make yes-RIGID + make clean-all + make NAME_OF_TARGET #<--("make ubuntu", "make g++", "make linux".) +---- + +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_misc/translocation/README_run.sh b/tools/moltemplate/examples/CG_misc/translocation/README_run.sh new file mode 100755 index 0000000000..7078918d5a --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/README_run.sh @@ -0,0 +1,28 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The "run.in.nvt" file is a LAMMPS input script containing +# references to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.nvt # Run a simulation at constant volume + +#or + +lmp_linux -i run.in.npt # Run a simulation at constant pressure + # (Note: Constant pressure conditions have not been + # well tested. The "run.in.npt" script may fail.) + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.nvt +#or +#mpirun -np 4 lmp_linux -i run.in.npt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/CG_misc/translocation/README_setup.sh b/tools/moltemplate/examples/CG_misc/translocation/README_setup.sh new file mode 100755 index 0000000000..acc5fbbaad --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/README_setup.sh @@ -0,0 +1,23 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_misc/translocation/README_visualize.txt b/tools/moltemplate/examples/CG_misc/translocation/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_misc/translocation/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_misc/translocation/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 0000000000..4a3f43234b --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,1995 @@ +PSF + + 1 !NTITLE + REMARKS VMD-generated NAMD/X-Plor PSF structure file + + 1716 !NATOM + 1 1 1 1 0.000000 10.0000 0 + 2 2 1 1 0.000000 10.0000 0 + 3 3 1 1 0.000000 10.0000 0 + 4 4 1 1 0.000000 10.0000 0 + 5 5 1 1 0.000000 10.0000 0 + 6 6 1 1 0.000000 10.0000 0 + 7 7 1 1 0.000000 10.0000 0 + 8 8 1 1 0.000000 10.0000 0 + 9 9 1 1 0.000000 10.0000 0 + 10 10 1 1 0.000000 10.0000 0 + 11 11 1 1 0.000000 10.0000 0 + 12 12 1 1 0.000000 10.0000 0 + 13 13 1 1 0.000000 10.0000 0 + 14 14 1 1 0.000000 10.0000 0 + 15 15 1 1 0.000000 10.0000 0 + 16 16 1 1 0.000000 10.0000 0 + 17 17 1 1 0.000000 10.0000 0 + 18 18 1 1 0.000000 10.0000 0 + 19 19 1 1 0.000000 10.0000 0 + 20 20 1 1 0.000000 10.0000 0 + 21 21 1 1 0.000000 10.0000 0 + 22 22 1 1 0.000000 10.0000 0 + 23 23 1 1 0.000000 10.0000 0 + 24 24 1 1 0.000000 10.0000 0 + 25 25 1 1 0.000000 10.0000 0 + 26 26 1 1 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b/tools/moltemplate/examples/CG_misc/translocation/images/walls+solvent+polymer_t=0.jpg new file mode 100644 index 0000000000..c1dcc4c186 Binary files /dev/null and b/tools/moltemplate/examples/CG_misc/translocation/images/walls+solvent+polymer_t=0.jpg differ diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/monomer.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/monomer.lt new file mode 100644 index 0000000000..4792580a97 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/monomer.lt @@ -0,0 +1,99 @@ + # ---------------------------------------------------------------------- + # -- General comment: -- + # -- The write() and write_once() commands create and append text to -- + # -- files (replacing variables beginning with @ or $ with counters.) -- + # -- File names beginning with "In " or "Data " are special. -- + # -- They will be pasted into the LAMMPS input script and -- + # -- data files which are generated by moltemplate. The syntax -- + # -- of these files is exactly the same as the syntax from the -- + # -- corresponding sections of a LAMMPS input script or data file. -- + # ---------------------------------------------------------------------- + + +Monomer { + + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:CA $mol:... @atom:CA 0.0 0.000 0.4000 0.00000 + $atom:R1 $mol:... @atom:R 0.0 0.000 1.000 1.000 + $atom:R2 $mol:... @atom:R 0.0 0.000 1.000 -1.000 + } + + # Note: The "..." in "$mol:..." tells moltemplate that this molecule may + # be a part of a larger molecule, and (if so) to use the larger + # parent object's molecule id number as it's own + + + # atom-type mass + + write_once("Data Masses") { + @atom:CA 13.0 + @atom:R 50.0 + } + + # atom-type atom-type epsilon sigma + + write_once("In Settings") { + pair_coeff @atom:CA @atom:CA 0.05 2.0 + pair_coeff @atom:R @atom:R 0.50 2.0 + } + + # bond-id bond-type atom-id1 atom-id2 + + write("Data Bonds") { + $bond:CR1 @bond:sidechain $atom:CA $atom:R1 + $bond:CR2 @bond:sidechain $atom:CA $atom:R2 + } + + write_once("In Settings") { + # bond-type k r0 + bond_coeff @bond:sidechain 30.0 1.2 + bond_coeff @bond:bb 30.0 2.0 # "bb" shorthand for "backbone" + } + + # Although there's no need to define angular interactions (because this + # "molecule" only contains two atoms), we define the settings for angles + # or dihedrals which might be present later when we build a polymer. + + write_once("In Settings") { + # angle-type k theta0 + angle_coeff @angle:backbone 50.00 160 + angle_coeff @angle:sidechain 50.00 120 + angle_coeff @angle:RCR 50.00 120 + # dihedral-type K1 K2 K3 K4 + dihedral_coeff @dihedral:backbn 1.411036 -0.271016 3.145034 0.0 + } + + # Rules for determining 3 and 4-body bonded interactions by type + + # angle-type atomType1 atomType2 atomType3 bondType1 bondType2 + + write_once("Data Angles By Type") { + @angle:backbone @atom:CA @atom:CA @atom:CA @bond:* @bond:* + @angle:sidechain @atom:CA @atom:CA @atom:R @bond:* @bond:* + @angle:RCR @atom:R @atom:CA @atom:R @bond:* @bond:* + } + + # dihedral-type AtomType1 AtomType2 AtomType3 AtomType4 bondType1 btyp2 btyp3 + + write_once("Data Dihedrals By Type") { + @dihedral:backbn @atom:CA @atom:CA @atom:CA @atom:CA @bond:* @bond:* @bond:* + } + +} # Monomer + + + + + + +# ------------------------------------------------------------------------- +# Heteropolymers: +# +# There is a similar example for heteropolymers which is distributed online +# bundled with the moltemplate software. It is named "2bead_heteropolymer", +# and it demonstrates how to share backbone (CA) atoms, bonds and angles +# (so that you don't have to define them seperately for each type of monomer). +# ------------------------------------------------------------------------- + diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/polymer.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/polymer.lt new file mode 100644 index 0000000000..d7ab89dc36 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/polymer.lt @@ -0,0 +1,35 @@ +import "monomer.lt" + +Polymer { + + # Make a chain of monomers + monomers = new Monomer [12].rot(180, 1,0,0).move(2.0, 0, 0) + + + # Now, link the monomers together this way: + write("Data Bonds") { + $bond:bb1 @bond:Monomer/bb $atom:monomers[0]/CA $atom:monomers[1]/CA + $bond:bb2 @bond:Monomer/bb $atom:monomers[1]/CA $atom:monomers[2]/CA + $bond:bb3 @bond:Monomer/bb $atom:monomers[2]/CA $atom:monomers[3]/CA + $bond:bb4 @bond:Monomer/bb $atom:monomers[3]/CA $atom:monomers[4]/CA + $bond:bb5 @bond:Monomer/bb $atom:monomers[4]/CA $atom:monomers[5]/CA + $bond:bb6 @bond:Monomer/bb $atom:monomers[5]/CA $atom:monomers[6]/CA + $bond:bb7 @bond:Monomer/bb $atom:monomers[6]/CA $atom:monomers[7]/CA + $bond:bb8 @bond:Monomer/bb $atom:monomers[7]/CA $atom:monomers[8]/CA + $bond:bb9 @bond:Monomer/bb $atom:monomers[8]/CA $atom:monomers[9]/CA + $bond:bb10 @bond:Monomer/bb $atom:monomers[9]/CA $atom:monomers[10]/CA + $bond:bb11 @bond:Monomer/bb $atom:monomers[10]/CA $atom:monomers[11]/CA + } + + create_var { $mol } # Create a molecule ID number for this polymer + + # This causes monomer[0], monomer[1], ... to share the same molecule counter + # because in the 2bead.lt file, the "..." in "$mol:..." preferentially looks + # for a counter of that type in a parent molecule or earlier ancestor. + +} # Polymer + + + +# Angle, dihedral and improper interactions will be generated +# automatically according to the instructions in "monomer.lt" diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent.lt new file mode 100644 index 0000000000..1073a58a14 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent.lt @@ -0,0 +1,23 @@ +###################### SOLVENT ######################### + +import "solvent_single.lt" + +# Fill the simulation box with a solvent. +# In this example, the solvent is made of many +# copies of "MoleculeA" (which has only one atom). + +solvent = new MoleculeA [12].move(3.0,0,0) + [12].move(0,3.0,0) + [12].move(0,0,3.0) + +# To start with a reasonable conformation, it's a good idea to delete the +# solvent where the walls or the polymer is going to be. Here we do it manually: + +delete solvent[*][*][2] # <-- 1st wall will go here +delete solvent[*][*][8] # <-- 2nd wall will go here +delete solvent[6-7][0-8][5-6] # <-- polymer will go here + +# Alternate notation: +# [a:b] notation also works, however the "b" is a strict upper bound... +# ...hence the last line is equivalent to "delete solvent[6:8][0:9][5:7]" +# [a*b] notation also works, and is equivalent to [a-b] diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent_single.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent_single.lt new file mode 100644 index 0000000000..8057e3c6fc --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent_single.lt @@ -0,0 +1,22 @@ +# The two files "solvent_single.lt" and "wall_single.lt" +# define two very simple molecules containing one atom each. +# Both atoms have a similar size (the have the same sigma parameter). + + +MoleculeA { + + # atomID molID atomType charge x y z + write("Data Atoms") { + $atom:a $mol:. @atom:a 0.0 0.0 0.0 0.0 + } + write_once("Data Masses") { + @atom:a 10.0 + } + write_once("In Settings") { + # i j epsilon sigma cutoff + pair_coeff @atom:a @atom:a 0.60 3.0 7.5 #<--attractive + group groupA type @atom:a #(Atoms of this type belong to the "A" group) + } + +} + diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/system.lt new file mode 100644 index 0000000000..90d60d3baa --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/system.lt @@ -0,0 +1,55 @@ + +# LAMMPS supports a large number of force-field styles. We must select +# which ones we need. This information belongs in the "In Init" section (and +# (you can specify it anywhere in your LT files, multiple times if you like). +# If different molecules use different force-field styles, you can use hybrid +# styles. (In this example the molecules share the same pair_style.) + +write_once("In Init") { + units real + atom_style full + bond_style harmonic + angle_style harmonic + dihedral_style opls + pair_style lj/cut 9.0 + # If you have charged molecules immersed in a salty implicit + # solvent, you might try something like this this instead: + # pair_style lj/cut/coul/debye 0.1 9.0 + pair_modify mix arithmetic + dielectric 80.0 + special_bonds lj 0.0 0.0 0.0 +} + + +write_once("Data Boundary") { + 0.0 36.0 xlo xhi + 0.0 36.0 ylo yhi + 0.0 36.0 zlo zhi +} + + +import "solvent.lt" + +import "walls.lt" + +import "polymer.lt" + +polymer = new Polymer +polymer.rot(-90.0, 0,0,1) # rotate it -90 degrees around the Y axis +polymer.move(19.5,22.5,16.5) # move it near the openning of the hole + + + +####################### Notes: ######################### +# +# In this example we deleted solvent and wall molecule objects. +# You can also delete a monomer inside the polymer. To do that use: +# delete polymer/monomers[6] +# You can also delete individual atoms, bonds, angles, dihedrals, & impropers +# from existing molecules. For example to delete an atom in the middle +# of the polymer try this. (Bonds and other interactions will also be removed.) +# delete polymer/monomers[6]/CA +# To delete a bond, try this +# delete polymer/bb6 +# Note: This will not delete the angular interactions. Delete them manually +# Note: In both cases the two molecule fragments will keep the same mol counter. diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/wall_single.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/wall_single.lt new file mode 100644 index 0000000000..79275a06b4 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/wall_single.lt @@ -0,0 +1,21 @@ +# The two files "solvent_single.lt" and "wall_single.lt" +# define two very simple molecules containing one atom each. +# Both atoms have a similar size (the have the same sigma parameter). + +MoleculeB { + + # atomID molID atomType charge x y z + write("Data Atoms") { + $atom:b $mol:. @atom:b 0.0 0.0 0.0 0.0 + } + write_once("Data Masses") { + @atom:b 10.0 + } + write_once("In Settings") { + # i j epsilon sigma cutoff + pair_coeff @atom:b @atom:b 0.05 3.0 7.5 #<--repulsive (approximately) + group groupB type @atom:b #(Atoms of this type belong to the "B" group) + } + +} + diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/walls.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/walls.lt new file mode 100644 index 0000000000..dcccac941e --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/walls.lt @@ -0,0 +1,23 @@ +####################### WALLS ########################## + +import "wall_single.lt" + +# Create a wall at position z=6.0 (6.0 = 2*3.0) + +wall1 = new MoleculeB [12].move(3.0, 0, 0) + [12].move(0, 3.0, 0) + +wall1[*][*].move(0,0,6.0) + +# Create a second wall at position z=24.0 (24.0 = 8*3.0) + +wall2 = new MoleculeB [12].move(3.0, 0, 0) + [12].move(0, 3.0, 0) + +wall2[*][*].move(0,0,24.0) + +# Now delete some of the molecules in "wall2" to create a hole. + +delete wall2[6-7][6-9] +delete wall2[5-8][7-8] + diff --git a/tools/moltemplate/examples/CG_misc/translocation/run.in.npt b/tools/moltemplate/examples/CG_misc/translocation/run.in.npt new file mode 100644 index 0000000000..1fb9ec9615 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/run.in.npt @@ -0,0 +1,70 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 1.0 +dump 1 all custom 500 traj_npt.lammpstrj id mol type x y z ix iy iz + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo 500 # time interval for printing out "thermo" data + + +velocity groupB zero angular +velocity groupB zero linear +# (I'm not sure if the two lines above are necessary, but they don't hurt.) + +# Only the groupB atoms are immobile. + +group mobile subtract all groupB + +# ------------------------- NPT --------------------------- + +# Set temp=300K, pressure=500bar, and equilibrate volume only in the z direction + +fix fMoveStuff mobile npt temp 300 300 100 z 500 500 1000.0 dilate mobile + +# ------ CONTROVERSIAL (see below): ------ + +fix Ffreezestuff groupB rigid/npt single temp 300 300 100 z 500 500 1000.0 force * off off off torque * off off off dilate mobile + +# -- Alternate npt rigid method -- +# I'm not sure which way is more correct, however +# this also seems to behave in a reasonable-looking way: +#fix Ffreezestuff groupB rigid single force * off off off torque * off off off dilate mobile +# +# The use of either "fix rigid" or "fix rigid/npt" to immobilize +# an object is somewhat controversial. Feel free to omit it. +#(Neither Trung or Steve Plimpton use rigid or rigid/npt for immobilizing +#molecules, but I noticed that at NPT, it does a better job of maintaining +# the correct volume. However "fix rigid" has changed since then (2011), +# so this may no longer be true. Please use this example with caution.) +# ---------------------------------------- + +# IMPORTANT for NPT: You must use "neigh_modify" to turn off calculation of the +# forces between immobilized atoms. +neigh_modify exclude group groupB groupB + +# The next two lines recalculate the temperature +# using only the mobile degrees of freedom: + +compute tempMobile mobile temp +compute pressMobile all pressure tempMobile + +thermo_style custom step c_tempMobile c_pressMobile temp press vol + +fix_modify fMoveStuff temp tempMobile + +run 60000 + +write_restart system_after_npt.rst diff --git a/tools/moltemplate/examples/CG_misc/translocation/run.in.nvt b/tools/moltemplate/examples/CG_misc/translocation/run.in.nvt new file mode 100644 index 0000000000..8ef52b1ed9 --- /dev/null +++ b/tools/moltemplate/examples/CG_misc/translocation/run.in.nvt @@ -0,0 +1,44 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 1.0 +dump 1 all custom 100 traj_nvt.lammpstrj id mol type x y z ix iy iz + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo 100 # time interval for printing out "thermo" data + + +# Optional: Improve efficiency by omitting the calcuation of interactions +# between immobile atoms. (Note: This is not optional under NPT conditions.) +neigh_modify exclude group groupB groupB + +# Only the groupB atoms are immobile. +group mobile subtract all groupB + +# The next two lines recalculate the temperature +# using only the mobile degrees of freedom: + +compute tempMobile mobile temp +compute pressMobile all pressure tempMobile + +# Integrate the equations of motion: +fix fMoveStuff mobile nvt temp 300.0 300.0 100.0 +fix_modify fMoveStuff temp tempMobile + + +run 200000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README.TXT b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README.TXT new file mode 100644 index 0000000000..33eeddda6e --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README.TXT @@ -0,0 +1,28 @@ +# -------- REQUIREMENTS: --------- +# 1) This example requires the "MANYBODY" package. +# As of 2012-9, it is included by default, but this may change in the future. +# If lammps complains of a missing pair style enter "make yes-MANYBODY" +# into the shell before compiling lammps. For details see: +# http://lammps.sandia.gov/doc/Section_start.html#start_3 +This is a relatively complex example containing two different types of +molecules, and a hybrid of Lennard-Jones and 3-body SW "pair" styles. + +The cyclododecane molecule uses the +TraPPE force field for hydrocarbon chains. +The parameters for the TraPPE force field are +in a file named "trappe1998.lt" which should be +located in the MOLTEMPLATE_PATH. +(See moltemplate installation instructions.) + +The water solvent is implemented using the 3-body single-particle +coarse-grained "mW" water model: +Molinero, V. and Moore, E.B., J. Phys. Chem. B 2009, 113, 4008-4016 + +More detailed instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step 2) +README_run.sh diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_run.sh b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_run.sh new file mode 100755 index 0000000000..8220a755c4 --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_run.sh @@ -0,0 +1,31 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data, system.in.sw +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.npt # minimization and simulation at constant pressure +lmp_linux -i run.in.nvt # minimization and simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation are ignored when beginning the simulation at constant volume. +# This can be fixed. Read "run.in.nvt" for equilibration instructions.) + + + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.npt +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_setup.sh b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_setup.sh new file mode 100755 index 0000000000..cb4d908984 --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_setup.sh @@ -0,0 +1,25 @@ + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt + + # Here we just want to make sure that the "mW" atom type is assigned to + # number "1". It should be by default, so usually you can leave out + # -a "@atom:/WatMW/mW 1". + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_visualize.txt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=0ps_LR.jpg b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=0ps_LR.jpg new file mode 100644 index 0000000000..5123dc7f60 Binary files /dev/null and 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a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/README.sh b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/README.sh new file mode 100755 index 0000000000..97b9f577d9 --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/README.sh @@ -0,0 +1,11 @@ +# Use this command to generate the LAMMPS input files: + +moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt + +# The -a argument insures that the "mW" atom type is assigned to "1". +# (This is necessary for the pair_coeff command to work. +# See system.lt for details.) + +# Note: To get rid of the annoying "atom_style unspecified warnings, +# use the "-atomstyle" command line argument, as in: +# moltemplate.sh -atomstyle full -a "@atom:/WatMW/mW 1" system.lt diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/cyclododecane.lt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/cyclododecane.lt new file mode 100644 index 0000000000..ceaa1c69d8 --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/cyclododecane.lt @@ -0,0 +1,55 @@ +import "trappe1998.lt" + +# The "trappe1998.lt" file is usually located in $MOLTEMPLATE_PATH (and is +# distributed with moltemplate. See the "Installation" section in the manual.) +# It contains definitions of the atoms "CH2", "CH3", and "CH4", as well +# as "saturated" bonds, and the parameters for (bonded/nonbonded) +# interactions between these atoms (all enclosed within the "TraPPE" namespace). + + +Cyclododecane { + + write('Data Atoms') { + $atom:C1 $mol:. @atom:TraPPE/CH2 0.0 0.00000 2.94118 0.0 + $atom:C2 $mol:. @atom:TraPPE/CH2 0.0 0.00000 2.54714 1.47059 + $atom:C3 $mol:. @atom:TraPPE/CH2 0.0 0.00000 1.47059 2.54714 + $atom:C4 $mol:. @atom:TraPPE/CH2 0.0 0.00000 0.0 2.94118 + $atom:C5 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -1.47059 2.54714 + $atom:C6 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -2.54714 1.47059 + $atom:C7 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -2.94118 0.0 + $atom:C8 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -2.54714 -1.47059 + $atom:C9 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -1.47059 -2.54714 + $atom:C10 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -0.0 -2.94118 + $atom:C11 $mol:. @atom:TraPPE/CH2 0.0 0.00000 1.47059 -2.54714 + $atom:C12 $mol:. @atom:TraPPE/CH2 0.0 0.00000 2.54714 -1.47059 + } + + # The "." in "$mol:." refers to the current object's molecule ID, + # and "@atom:TraPPE/CH2" refers to the "CH2" atom-type defined in TraPPE + + write('Data Bonds') { + $bond:bond1 @bond:TraPPE/saturated $atom:C1 $atom:C2 + $bond:bond2 @bond:TraPPE/saturated $atom:C2 $atom:C3 + $bond:bond3 @bond:TraPPE/saturated $atom:C3 $atom:C4 + $bond:bond4 @bond:TraPPE/saturated $atom:C4 $atom:C5 + $bond:bond5 @bond:TraPPE/saturated $atom:C5 $atom:C6 + $bond:bond6 @bond:TraPPE/saturated $atom:C6 $atom:C7 + $bond:bond7 @bond:TraPPE/saturated $atom:C7 $atom:C8 + $bond:bond8 @bond:TraPPE/saturated $atom:C8 $atom:C9 + $bond:bond9 @bond:TraPPE/saturated $atom:C9 $atom:C10 + $bond:bond10 @bond:TraPPE/saturated $atom:C10 $atom:C11 + $bond:bond11 @bond:TraPPE/saturated $atom:C11 $atom:C12 + $bond:bond12 @bond:TraPPE/saturated $atom:C12 $atom:C1 + } + +} # Cyclododecane + + +# coordinates in the "Data Atoms" section generated by this python code: +# from math import * +# bond_length=1.54 +# N=12 +# R=(N*bond_length)/(2*pi) +# for i in range(0,N): +# print('$atom:C'+str(i+1)+' $mol:... @atom:TraPPE/CH2 0.0 0.00000 '+ +# str(round(R*cos(i*2*pi/N),5))+' '+str(round(R*sin(i*2*pi/N),5))) diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/system.lt new file mode 100644 index 0000000000..4a7063491b --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/system.lt @@ -0,0 +1,62 @@ +# This is a relatively complex example containing two different types of +# molecules, and a hybrid of Lennard-Jones and 3-body SW "pair" styles. + +import "watmw.lt" +import "cyclododecane.lt" + +write_once("Data Boundary") { + 0.000000 48.000 xlo xhi + 0.000000 48.000 ylo yhi + 0.000000 48.000 zlo zhi +} + +wat = new WatMW [12].move(0, 0, 4.0) + [12].move(0, 4.0, 0) + [12].move(4.0, 0, 0) + +cyclododecane = new Cyclododecane [4].move(0, 0, 12.0) + [4].move(0, 12.0, 0) + [4].move(12.0, 0, 0) + +# (Move them by (6.0,6.0,6.0) to avoid overlap with the water.) +cyclododecane[*][*][*].move(6.0,6.0,6.0) + +write_once("In Init") { + # -- Tell LAMMPS we want to use two different pair styles + # -- (This overrides earlier settings.) + pair_style hybrid sw lj/charmm/coul/charmm 9.0 11.0 9.0 11.0 +} + + +write_once("In Settings") { + # -- Now indicate which atom type(s) are simulated using the "sw" pair style + # -- In this case only one of the atom types is used (the mW water "atom"). + + pair_coeff * * sw system.in.sw mW NULL NULL NULL + + # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so + # -- the atoms are identified by order in the list, not by name. (The "mW" + # -- refers to to an identifier in the system.in.sw file, not watmw.lt.) + # -- This command says that the first atom type corresponds to the "mW" + # -- atom in system.in.sw, and to ignore the remaining three atom types + # -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt. + # -- We don't want to use the "sw" force field for interactions involving + # -- these atom types, so we put "NULL" there.) + # -- Note: For this to work, you should probably run moltemplate this way: + # -- moltemplate.sh -a "@atom:WatMW/mW 1" system.lt + # -- This assigns the atom type named @atom:WatMW/mW to 1 (the first atom) +} + + + +# -- Somewhere we must eventually define interactions +# -- between atoms from different molecule types + +write_once("In Settings") { + pair_coeff @atom:WatMW/mW @atom:TraPPE/CH2 lj/charmm/coul/charmm 0.11914784667210733 3.558 + pair_coeff @atom:WatMW/mW @atom:TraPPE/CH3 lj/charmm/coul/charmm 0.17390830404497651 3.458 + pair_coeff @atom:WatMW/mW @atom:TraPPE/CH4 lj/charmm/coul/charmm 0.21371654257637612 3.448 +} + + + diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/trappe1998.lt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/trappe1998.lt new file mode 100644 index 0000000000..9bcc80cb1c --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/trappe1998.lt @@ -0,0 +1,50 @@ +# This file stores complete LAMMPS data for the TraPPE model of saturated +# hydrocarbon chains. In this "united-atom" model, each methyl group is +# represented by a single atom. Forces between "atoms" are taken from the +# TraPPE force-field. (J Phys Chem B, 1998, volume 102, pp.2569-2577) + +TraPPE { + + write_once("In Init") { + # -- Default styles for "TraPPE" -- + units real + atom_style full + # (Hybrid force field styles were used for portability.) + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid opls + improper_style none + pair_style hybrid lj/charmm/coul/charmm 9.0 11.0 9.0 11.0 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom:CH2 14.1707 + @atom:CH3 15.2507 + @atom:CH4 16.3307 + } + + write_once("Data Angles By Type") { + @angle:backbone @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated + } + + write_once("Data Dihedrals By Type") { + @dihedral:backbone @atom:CH? @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated @bond:saturated + } + + write_once("In Settings") { + pair_coeff @atom:CH2 @atom:CH2 lj/charmm/coul/charmm 0.091411522 3.95 + pair_coeff @atom:CH3 @atom:CH3 lj/charmm/coul/charmm 0.194746286 3.75 + pair_coeff @atom:CH4 @atom:CH4 lj/charmm/coul/charmm 0.294106636 3.73 + bond_coeff @bond:saturated harmonic 120.0 1.54 + angle_coeff @angle:backbone harmonic 62.0022 114 + dihedral_coeff @dihedral:backbone opls 1.411036 -0.271016 3.145034 0.0 + } + + write_once("In Settings") { + group TraPPE type @atom:CH2 @atom:CH3 @atom:CH4 + } + +} # class TraPPE + diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/version_more_comments/system.lt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/version_more_comments/system.lt new file mode 100644 index 0000000000..34bdfead77 --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/version_more_comments/system.lt @@ -0,0 +1,80 @@ +# This is a relatively complex example containing two different types of +# molecules, and a hybrid of Lennard-Jones and 3-body SW "pair" styles. + +import "watmw.lt" +import "cyclododecane.lt" + +write_once("Data Boundary") { + 0.000000 48.000 xlo xhi + 0.000000 48.000 ylo yhi + 0.000000 48.000 zlo zhi +} + +wat = new WatMW [12].move(0, 0, 4.0) + [12].move(0, 4.0, 0) + [12].move(4.0, 0, 0) + +cyclododecane = new Cyclododecane [4].move(0, 0, 12.0) + [4].move(0, 12.0, 0) + [4].move(12.0, 0, 0) + +# (Move them by (6.0,6.0,6.0) to avoid overlap with the water.) +cyclododecane[*][*][*].move(6.0,6.0,6.0) + +write_once("In Init") { + # -- Tell LAMMPS we want to use two different pair styles + # -- (This overrides earlier settings.) + pair_style hybrid sw lj/charmm/coul/charmm 9.0 11.0 9.0 11.0 +} + + + +write_once("In Settings") { + # -- Now indicate which atom type(s) are simulated using the "sw" pair style + # -- In this case only one of the atom types is used (the mW water "atom"). + + pair_coeff * * sw system.in.sw mW NULL NULL NULL + + # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so + # -- the atoms are identified by order in the list, not by name. (The "mW" + # -- refers to to an identifier in the system.in.sw file, not watmw.lt.) + # -- This command says that the first atom type corresponds to the "mW" + # -- atom in system.in.sw, and to ignore the remaining three atom types + # -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt. + # -- We don't want to use the "sw" force field for interactions involving + # -- these atom types, so we put "NULL" there.) + # + # For this to work, the first atom type (assigned to "1") + # must refer to the "mW" atom type (defined in watmw.lt). + # (This is why we included "watmw.lt" first, to insure that the + # atom counters in WatMW are assinged first, starting with 1.) + # Alternately we can further insure that this happens, it's + # a good idea to run moltemplate.sh using the "-a" argument: + # moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt + # This assigns the atom type named @atom:/WatMW/mW to 1 +} + + + + +# -- Somewhere we must eventually define interactions +# -- between atoms from different molecule types +# -- Now define interactions between DIFFERENT molecules +# Note: In the SPC/E model, the epsilon,sigma parameters for water is 0.1553 +# 3.166. As a crude guess, I chose the LJ parameters for the interaction +# between water & the CH2,CH3,CH4 atoms using Lorentz-Berthelot mixing rules + +write_once("In Settings") { + pair_coeff @atom:WatMW/mW @atom:TraPPE/CH2 lj/charmm/coul/charmm 0.11914784667210733 3.558 + pair_coeff @atom:WatMW/mW @atom:TraPPE/CH3 lj/charmm/coul/charmm 0.17390830404497651 3.458 + pair_coeff @atom:WatMW/mW @atom:TraPPE/CH4 lj/charmm/coul/charmm 0.21371654257637612 3.448 +} + + + + + + + + + diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/watmw.lt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/watmw.lt new file mode 100644 index 0000000000..c7aaecebbc --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/watmw.lt @@ -0,0 +1,54 @@ +# This file stores LAMMPS data for the "mW" water model. +# (Molinero, V. and Moore, E.B., J. Phys. Chem. B 2009, 113, 4008-4016) +# +# In this model, each water molecule is represented by a single "mW" particle. +# These particles interact with their neighbors via 3-body Stillinger-Weber +# forces whose parameters are tuned to mimic directional hydrogen-bonding +# in liquid water (as well as hexagonal ice, type II ice, and +# low-density super-cooled liquid/amorphous water phases). + +WatMW { + write("Data Atoms") { + $atom:mW $mol:. @atom:mW 0.0 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom:mW 18.02 + } + + write_once("system.in.sw") { + mW mW mW 6.189 2.3925 1.8 23.15 1.2 -0.333333333 7.049556277 0.602224558 4 0 0 + } + + write_once("In Init") { + # -- Default styles for "WatMW" -- + units real + pair_style sw + } + + write_once("In Settings") { + # --Now indicate which atom type(s) are simulated using the "sw" pair style + # -- In this case only one of the atom types is used (the mW water "atom"). + + pair_coeff * * sw system.in.sw mW NULL NULL NULL + + # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so + # -- the atoms are identified by order in the list, not by name. (The "mW" + # -- refers to to an identifier in the system.in.sw file, not watmw.lt.) + # -- This command says that the first atom type corresponds to the "mW" + # -- atom in system.in.sw, and to ignore the remaining three atom types + # -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt. + # -- We don't want to use the "sw" force field for interactions involving + # -- these atom types, so we put "NULL" there.) + # -- Note: For this to work, you should probably run moltemplate this way: + # -- moltemplate.sh -a "@atom:WatMW/mW 1" system.lt + # -- This assigns the atom type named @atom:WatMW/mW to 1 (the first atom) + } + + # -- optional -- + + write_once("In Settings") { + group WatMW type @atom:mW #(Atoms of this type belong to the "WatMW" group) + } + +} # WatMW diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.npt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.npt new file mode 100644 index 0000000000..59d5ce9f87 --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.npt @@ -0,0 +1,58 @@ +# run.in.npt +# +# -- Usage -- +# +# lmp_g++ -i run.in.npt +# (assuming lmp_g++ is the name of your lammps binary) +# +# -- Prerequisite Input Files: -- +# systen.data, system.in.init, system.in.settings, system.in.sw +# +# You can generate these files with this command: +# moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt +# --------------------------------- + +# ----- Init Section ----- + + +include system.in.init + + +# ----- Atom Definition Section ----- + + +read_data system.data + + +# ----- Settings Section ----- + + +include system.in.settings + + +# ----- Run Section ----- + + + +# -- minimization protocol -- + +# Note: The minimization step is not necessary in this example. However +# in general, it's always a good idea to minimize the system beforehand. + +minimize 1.0e-5 1.0e-7 100000 400000 + + +# -- simulation protocol -- + + +timestep 2.0 # <- This can be increased to 5.0 or 10.0 for bulk water +dump 1 all custom 500 traj_npt.lammpstrj id mol type x y z ix iy iz +fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 + + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo 500 # time interval for printing out "thermo" data + +run 200000 + +write_restart system_after_npt.rst diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.nvt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.nvt new file mode 100644 index 0000000000..9d499517dc --- /dev/null +++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.nvt @@ -0,0 +1,78 @@ +# run.in.nvt +# +# -- Usage -- +# +# lmp_g++ -i run.in.nvt +# (assuming lmp_g++ is the name of your lammps binary) +# +# -- Prerequisite Input Files: -- +# systen.data, system.in.init, system.in.settings, system.in.sw +# +# You can generate these files with this command: +# moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt +# --------------------------------- + + +# -- init section -- + + +include system.in.init + + + +# -- atom definition section -- + +# Normally, I would minimize the system and equilibrate the system at constant +# pressure and temperature beforehand. If you run lammps with "run.in.npt", +# it will generate a restart file "system_after_npt.rst" with reasonable +# coordinates at that temperature and pressure. Then we could load it now: +# +#read_restart system_after_npt.rst +# +# Unfortunately the LAMMPS "read_restart" command has been undependable over +# the past year (2012), and I feel it is safer to remove it from the examples. +# Instead, for this example, I just read the raw coordinates generated by +# moltemplate (and the default volume). (I get fewer questions this way.) +# However you should never run any liquid simulations at constant volume without +# pressure equilibration first. Hopefully in the future "read_restart" will +# work. Otherwise try "read_dump", "dump2data.py", or "restart2data". + + +read_data system.data + + + +# -- settings section -- + + +include system.in.settings + + +# -- run section -- + + +timestep 2.0 +dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz +dump 2 TraPPE custom 1000 traj_alkane_nvt.lammpstrj id mol type x y z ix iy iz +fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 + +# The following commands are useful if you want to calculate the distribution +# of alkane-chain radius-of-gyration at a given temperature & pressure. +#compute cRg TraPPE gyration +#variable vRg equal c_cRg +#compute cPE all pe +#variable vPE equal c_cPE +#fix FprintPE all print 1000 "${vPE}" file U.dat +#fix FprintRg all print 1000 "${vRg}" file Rg.dat + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo 1000 # time interval for printing out "thermo" data +#thermo_modify flush yes + +restart 100000 restart_nvt + +run 1000000 + +write_restart system_after_nvt.rst + + diff --git a/tools/moltemplate/examples/README.TXT b/tools/moltemplate/examples/README.TXT new file mode 100644 index 0000000000..0ecddbbbd4 --- /dev/null +++ b/tools/moltemplate/examples/README.TXT @@ -0,0 +1,24 @@ +These are examples for the "moltemplate" molecule builder for LAMMPS. +http://www.moltemplate.org + +Each directory contains one or more examples. + +Each example directory contains: + + images/ This folder has pictures of the molecules in the system + moltemplate_files/ This folder contains LT files and other auxiliary files + README_setup.sh Instructions for how to use moltemplate (executable) + README_visualize.txt Instructions for viewing in DATA/DUMP files in VMD + + ...and one or more LAMMPS input scripts with names like + + run.in.min + run.in.npt + run.in.nvt + +You can run these scripts using + lmp_linux -i run.in.npt +(The name of your lammps binary, "lmp_linux" in this example, may vary. + Sometimes, these scripts must be run in a certain order. For example + it may be necessary to run run.in.min to minimize the system before + you can run the other scripts. These files have not been optimized.) diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README.TXT b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README.TXT new file mode 100644 index 0000000000..355fe42831 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README.TXT @@ -0,0 +1,54 @@ +NOTE: This example requires the "Al99.eam.alloy" file. + (It was not included in this directory because if its large size.) + As of 2012-11, I was able to obtain it here: + http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy + Copy it to the directory containing this README file. +------------------------------------------------------------------------ +This example shows an alternative way to setup the +aluminum crystal loading simulation described here: +http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression +by Mark Tschopp and Nathan R. Rhodes +For additional backgroumd information, please consult that web page. + +In this example, I use moltemplate to build a "DATA" file for this system. +(I can't think of a compelling reason to do this for simple simulations like +this. But this approach might be useful if you want to artificially create +unusual structures out of aluminum crystals, or mix them with other molecules. +I created this example in response to a user request.) + + + --- To build the system --- + +Carry out the instructions in README_setup.sh, +to generate the LAMMPS DATA file and input scripts you need: +system.data, system.in.init, system.in.settings. +(The run.in script contains references to these files.) + + + --- To run LAMMPS, try a command like: --- + +lmp_linux -i run.in + + or (if you have mpi installed) + +mpirun -np 4 lmp_linux -i run.in + +This will create an ordinary LAMMPS dump file you can visualize with VMD +traj.lammpstrj (See README_visualize.txt) + +It will also create a number of other files, such as: +dump.comp_0.cfg +dump.comp_500.cfg +dump.comp_20000.cfg +Al_comp_100.def1.txt + +The dump.comp_*.cfg files can be visualized using +AtomEye if you have AtomEye and ImageJ installed. +The procedure for doing this is explained in the original tutorial at: +http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression + +The "Al_comp_100.def1.txt" file is a four-column text file containing: +column 1: v_strain = (lx - v_L0)/v_L0 +column 2: -pxx/10000 (diagonal components of the stress tensor) +column 3: -pyy/10000 +column 4: -pzz/10000 diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README_setup.sh new file mode 100755 index 0000000000..22eb8c4357 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README_setup.sh @@ -0,0 +1,29 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -atomstyle full system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # We will also need the "Al99.eam.alloy" file: + #cp -f Al99.eam.alloy ../ + # This file was (can be) downloaded from: + # http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy + + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCell_LR.jpg b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCell_LR.jpg new file mode 100644 index 0000000000..bf07914dac Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCell_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCrystal10x10x10_t=0steps_LR.jpg b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCrystal10x10x10_t=0steps_LR.jpg new file mode 100644 index 0000000000..8650cf5cb0 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCrystal10x10x10_t=0steps_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCrystal10x10x10_t=20000steps_LR.jpg b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCrystal10x10x10_t=20000steps_LR.jpg new file mode 100644 index 0000000000..582cf5fe6d Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCrystal10x10x10_t=20000steps_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/README.sh b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/README.sh new file mode 100755 index 0000000000..64f350f641 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/README.sh @@ -0,0 +1,22 @@ +# This example shows an alternative way to setup the +# aluminum crystal loading simulation described here: +# http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression +# by Mark Tschopp and Nathan R. Rhodes +# For additional backgroumd information, please consult that web page. +# +# In this example, I use moltemplate to build a "DATA" file for this system. +# (I can't think of a compelling reason to do this for simple simulations like +# this. But this approach might be useful if you want to artificially create +# unusual structures out of aluminum crystals, or mix them with other molecules. +# I created this example in response to a user request.) +# +# Use these commands to generate the LAMMPS input script and data file: + +moltemplate.sh system.lt + +# This will generate system.data, system.in.init, system.in.settings. +# In addition to will need to download "Al99.eam.alloy" file. +# (It was not included in this directory because if its large size.) +# As of 2012-11, I was able to obtain it here: +# http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy + diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/al_cell.lt b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/al_cell.lt new file mode 100644 index 0000000000..3054a45e01 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/al_cell.lt @@ -0,0 +1,64 @@ +# "AlCell" defines the 4-atom FCC unit cell +# of Aluminum (with a 4.05 angstrom spacing) + +AlCell { + + # AtomID MolID(IGNORE!) AtomType Charge X Y Z + + write("Data Atoms") { + $atom:AlC $mol:... @atom:Al 0.0 0.000 0.000 0.000 + $atom:AlX $mol:... @atom:Al 0.0 0.000 2.025 2.025 + $atom:AlY $mol:... @atom:Al 0.0 2.025 0.000 2.025 + $atom:AlZ $mol:... @atom:Al 0.0 2.025 2.025 0.000 + } + + write_once("In Init") { + units metal + atom_style full # <- Requires each atom has a MolID and Charge. + # This is not necessary. (Why use "full"? + # The "full" atom style is useful if you want to + # mix the aluminum with other molecules later. + # Otherwise, just use "atom_style atomic", and + # and remove the 2nd and 4th columns above.) + pair_style eam/alloy + } + + write_once("In Settings") { + pair_coeff * * Al99.eam.alloy Al + } + + write_once("Data Masses") { + @atom:Al 27.0 + } + +} # AlCell + + + + + +# Here is an alternate way to define AlCell +# using "scale(4.05)" to select the lattice spacing: +# +#FccCell { +# write("Data Atoms") { +# $atom:AlC $mol:... @atom:Al 0.0 0.0 0.0 0.0 +# $atom:AlX $mol:... @atom:Al 0.0 0.0 0.5 0.5 +# $atom:AlY $mol:... @atom:Al 0.0 0.5 0.0 0.5 +# $atom:AyZ $mol:... @atom:Al 0.0 0.5 0.5 0.0 +# } +# write_once("Data Masses") { +# @atom:Al 27.0 +# } +# write_once("In Init") { +# units metal +# atom_style full +# pair_style eam/alloy +# } +# write_once("In Settings") { +# pair_coeff * * Al99.eam.alloy Al +# } +#} +# +#AlCell = FccCell.scale(4.05) +# diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/system.lt new file mode 100644 index 0000000000..f813c6f662 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/system.lt @@ -0,0 +1,35 @@ + +import "al_cell.lt" # <- this defines the unit cell for aluminum + +# Periodic boundary conditions: +write_once("Data Boundary") { + 0.0 40.50 xlo xhi + 0.0 40.50 ylo yhi + 0.0 40.50 zlo zhi +} + +# The next command generates an array of 10x10x10 AlCell unit cells with +# spacing 4.05 Angstroms. + +unitcells = new AlCell [10].move(0.00, 0.00, 4.05) + [10].move(0.00, 4.05, 0.00) + [10].move(4.05, 0.00, 0.00) + + + + + + + + + + + + +################################################################ +# The next command is not necessary: +# + create_var { $mol } # <-This forces all of the Al atoms in the crystal +# # to share the same molecule ID number. +# # Molecule ID numbers are not necessary. Ignore this. +# diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/run.in b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/run.in new file mode 100644 index 0000000000..677cc60cab --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/run.in @@ -0,0 +1,76 @@ +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- +# +# The run-settings below were stolen from: +# +# http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression + + +compute csym all centro/atom fcc +compute peratom all pe/atom + +# EQUILIBRATION +reset_timestep 0 +timestep 0.001 +velocity all create 300 12345 mom yes rot no +fix 1 all npt temp 300 300 1 iso 0 0 1 drag 1 + +# Set thermo output +thermo 1000 +thermo_style custom step lx ly lz press pxx pyy pzz pe temp + +# Run for at least 10 picosecond (assuming 1 fs timestep) +run 20000 +unfix 1 + +# Store final cell length for strain calculations +variable tmp equal "lx" +variable L0 equal ${tmp} +print "Initial Length, L0: ${L0}" + +###################################### +# DEFORMATION +reset_timestep 0 + +fix 1 all npt temp 300 300 1 y 0 0 1 z 0 0 1 drag 1 +variable srate equal 1.0e10 +variable srate1 equal "-v_srate / 1.0e12" +fix 2 all deform 1 x erate ${srate1} units box remap x + +# Output strain and stress info to file +# for units metal, pressure is in [bars] = 100 [kPa] = 1/10000 [GPa] +# p2, p3, p4 are in GPa +variable strain equal "(lx - v_L0)/v_L0" +variable p1 equal "v_strain" +variable p2 equal "-pxx/10000" +variable p3 equal "-pyy/10000" +variable p4 equal "-pzz/10000" +fix def1 all print 100 "${p1} ${p2} ${p3} ${p4}" file Al_comp_100.def1.txt screen no + +# Use cfg for AtomEye +dump dAtomEye all cfg 250 dump.comp_*.cfg id type xs ys zs c_csym c_peratom fx fy fz +dump_modify dAtomEye element Al + +# For users without AtomEye (like me), I decided to create a regular dump file: +dump dCoords all custom 250 traj.lammpstrj id type x y z ix iy iz + +# Display thermo +thermo 1000 +thermo_style custom step v_strain temp v_p2 v_p3 v_p4 ke pe press + +run 20000 + +###################################### +# SIMULATION DONE +print "All done" diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_FIRST.TXT b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_FIRST.TXT new file mode 100644 index 0000000000..80ab9c443e --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_FIRST.TXT @@ -0,0 +1,83 @@ +########################################################### +# Interaction of a carbon nanotube with a pair of "mystery +# molecules" (extracted from the cnat-cnt.data/in files). +########################################################### +# Author: Aysun Itai and Andrew Jewett + +This example uses "ltemplify.py" to create molecule templates out +of two different molecules in a pre-existing LAMMPS IN/DATA file. +Then I show how to use "moltemplate.sh" to make copies of these +molecules and to move and rotate them (creating new LAMMPS IN/DATA files). + + Disclaimer: +The molecules in this example are not physically realistic. +The purpose of this example is to demonstrate ltemplify usage. + + REQUIRED INPUT FILES + +cnad-cnt.data cnad-cnt.in system.lt + + cnad-cnt.data + This is a LAMMPS data file containing the coordinates and the topology + for a system combining the two molecules together. ltemplify will extract + molecules from this file, one at a time. + + cnad-cnt.in + This file contains force-field parameters and old run settings for the system. + (We ignore the run settings in this file.) The force-field parameters in + the "cnad-cnt.in" file are only necessary because we are going to build + a completely new set of simulation input files. (We are not only going to + rotate them and duplicate the molecules.) ltemplify.py will extract the + force field parameters from this file. This approach allows us to combine + these molecules with other types of molecules later on.) + + system.lt + The "system.lt" contains the instructions what we will do with these molecules + after ltemplify.py has converted them into .LT format. In this example + it contains instructions for rotating and copying the two molecules, + (It also defines the periodic boundary conditions.) + + OUTPUT FILES + +cnad.lt +cnt.lt + +These files are referenced in system.lt. +Running moltemplate.sh on system.lt (using "moltemplate.sh system.lt") +creates new LAMMPS data and input files: +system.data, system.in, system.in.init, system.in.settings +(These files are referenced in run.in.nvt.) + +You can run a simulation from the files created by moltemplate using + +lmp_linux -i run.in.nvt + +NOTE: BECAUSE ALL OF THE ORIGINAL FORCE FIELD PARAMETERS WERE INTENTIONALLY + ALTERED, THE SYSTEM WILL MOVE IN A VERY UNREALISTIC WAY WHEN SIMULATED. + (This was done to protect the original source of the files.) + The goal of this example is only to demonstrate how to use + "ltemplify.py" to convert lammps input and data files into + LT format and back again.) + + ----------- + +Instructions: +Execute the commands in: + +step 1) +README_run_ltemplify.sh + +and then + +step 2) +README_run_moltemplate.sh + +step 3) OPTIONAL + +To run a short LAMMPS simulation, you can use the "in.nvt" file, for example: + +$LAMMPS_BINARY -i run.in.nvt + +where "$LAMMPS_BINARY" is the name of the command you use to invoke lammps +(such as lmp_linux, lmp_g++, lmp_mac, lmp_ubuntu, lmp_cygwin, etc...). + ----------- diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_lammps.sh b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_lammps.sh new file mode 100755 index 0000000000..813c406c0e --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_lammps.sh @@ -0,0 +1,16 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The "run.in.nvt" LAMMPS input script links to the input +# scripts and data files you hopefully have created earlier +# with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_run_moltemplate.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps this way: + +lmp_linux -i run.in.nvt + +# NOTE: BECAUSE ALL OF THE ORIGINAL FORCE FIELD PARAMETERS WERE INTENTIONALLY +# REMOVED, THE SYSTEM WILL MOVE IN A VERY UNREALISTIC WAY. diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_ltemplify.sh b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_ltemplify.sh new file mode 100755 index 0000000000..4bb42d7ea6 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_ltemplify.sh @@ -0,0 +1,13 @@ +#!/bin/sh + +# Aysun Itai's LAMMPS files contain two molecules: + +# The CNAD molecule has molecule-id 1 + +ltemplify.py -name CNAD -molid "1" cnad-cnt.in cnad-cnt.data > cnad.lt + +# The CNT (carbon nanotube) corresponds to molecule-id 2 +ltemplify.py -name CNT -molid "2" cnad-cnt.in cnad-cnt.data > cnt.lt + +# This will extract both molecules and save them as separate .LT files. +# (We can include these files later when preparing new simulations.) diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_moltemplate.sh b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_moltemplate.sh new file mode 100755 index 0000000000..c99d4b9729 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_moltemplate.sh @@ -0,0 +1,18 @@ +# --- Running Moltemplate --- +# -- Prerequisites: -- +# The "system.lt" moltemplate file links to other ".lt" files +# files you hopefully have created earlier when you ran "ltemplify.py: +# cnad.lt and cnt.lt +# If not, carry out the instructions in "README_run_ltemplify.sh". + +moltemplate.sh system.lt + +# This will generate various files with names ending in *.in* and *.data. +# These files are the input files directly read by LAMMPS. + +# Optional: +# The "./output_ttree/" directory is full of temporary files generated by +# moltemplate. They can be useful for debugging, but are usually thrown away. + +rm -rf output_ttree/ + diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_visualize.txt new file mode 100644 index 0000000000..3b9be3e9c3 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_visualize.txt @@ -0,0 +1,50 @@ + + ------- To view the trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + + +Later, to Load a trajectory in VMD: + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it + +----- Wrap the coordinates to the unit cell + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Enter: + + DISCLAIMER: I'M NOT SURE THESE COMMANDS ARE CORRECT. + LOOKUP "pbctools" FOR DETAILS. + + pbc wrap -compound res -all + pbc box + +3) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.data b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.data new file mode 100644 index 0000000000..1f18ff4aef --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.data @@ -0,0 +1,1157 @@ +Created by Aysun Itai and modified by Andrew Jewett +NOTE: This file has been extensively modified. +Only the bond connectivity and atomic positions are accurate. + + 101 atoms + 134 bonds + 252 angles + 457 dihedrals + 0 impropers + + 16 atom types + 24 bond types + 50 angle types + 78 dihedral types + 0 improper types + + 0 50 xlo xhi + 0 50 ylo yhi + 0 50 zlo zhi + +Masses + + 1 10.0 + 2 10.0 # atom type names often appear + 3 10.0 # in the comments follwing + 4 10.0 # each line in the Masses section + 5 10.0 + 6 10.0 + 7 10.0 + 8 10.0 + 9 10.0 + 10 10.0 + 11 10.0 + 12 10.0 + 13 10.0 + 14 10.0 + 15 10.0 + 16 10.0 + +Atoms + +1 2 1 0.000000 12.345 10.000 4.328 +2 2 1 0.000000 12.031 11.173 5.037 +3 2 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@@ -0,0 +1,49 @@ +#Created by Aysun Itai and modified by Andrew Jewett +# NOTE: This file has been extensively modified. +# Only the bond connectivity and atomic positions are accurate. + +units real + +neigh_modify delay 2 every 1 + +atom_style full +bond_style harmonic +angle_style charmm +dihedral_style charmm +pair_style lj/charmm/coul/charmm 8.0 10.0 +pair_modify mix arithmetic + +read_data cnad-cnt.data + +pair_coeff 1 1 0.02 4.0 +pair_coeff 2 2 0.02 1.0 # atoms will not interact sterically +pair_coeff 3 3 0.02 2.0 # in this version of the file. +pair_coeff 4 4 0.02 2.0 # (All pair forces and atom names removed) +pair_coeff 5 5 0.02 2.0 +pair_coeff 6 6 0.02 3.0 +pair_coeff 7 7 0.02 3.0 +pair_coeff 8 8 0.02 3.0 +pair_coeff 9 9 0.02 4.0 +pair_coeff 10 10 0.02 4.0 +pair_coeff 11 11 0.02 4.0 +pair_coeff 12 12 0.02 4.0 +pair_coeff 13 13 0.02 3.0 +pair_coeff 14 14 0.02 3.0 +pair_coeff 15 15 0.02 3.0 +pair_coeff 16 16 0.02 3.0 + +group cnt type 1 +group cnad type 2-16 + +displace_atoms 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0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 + + 1 0 !NGRP + 0 0 0 + diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/run.in.nvt new file mode 100644 index 0000000000..5c1d2d4172 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/run.in.nvt @@ -0,0 +1,46 @@ +########################################################### +# Interaction of a carbon nanotube with a pair of mystery +# molecules (extracted from the cnat-cnt.data/in files). +########################################################### +# +# define the system being simulated: + +# -- init section -- +include system.in.init + +# -- atom definition section -- + +read_data system.data + +# -- settings section -- + +include system.in.settings + +# -- run section -- + + +timestep 0.05 +dump 1 all custom 2000 traj_nvt.lammpstrj id mol type x y z ix iy iz + +# The Nose-Hoover thermostat used with "fix nvt" can produce very odd-looking +# dynamics in dilute systems with few atoms (such as this one). +# Commenting this next line out: + +# fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 + +# Alternately, I receive fewer questions if I use langevin/nve instead: +fix fxlan all langevin 300.0 300.0 1000.0 48279 scale 3 1.5 +fix fxnve all nve + + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo 500 # time interval for printing out "thermo" data +#thermo_modify flush yes + +#restart 1000000 restart_nvt + +run 500000 + +write_restart system_after_nvt.rst + + diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/system.lt b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/system.lt new file mode 100644 index 0000000000..70fdb7548b --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/system.lt @@ -0,0 +1,29 @@ +#Define the CNT and CNAD molecules, by including the files which define them +import cnt.lt +import cnad.lt + +# The cnt's center was originally at position 10,10,10, +# so I moved it back to the origin +cnt = new CNT.move(-10,-10,-10) + +# Rotation around the center of mass does not work (yet), +# so instead you have to move the molecule to the origin, +# rotate it, and move it back to where you want it. +# That's why the next line contains move().rot().move() +# I'll add center-of-mass rotation as a later feature. + +cnad1 = new CNAD.move(0.611276,-0.0237931,-0.0487586).rot(90,0,1,0).move(-7,0,0) +cnad2 = new CNAD.move(0.611276,-0.0237931,-0.0487586).rot(-90,0,1,0).move(7,0,0) + + +# You can leave the periodic boundary conditions unspecified +# and change them later, OR you can declare them +# using the "write_once("Data Boundary") {}" command: + +write_once("Data Boundary") +{ + 0 50.0 xlo xhi + 0 50.0 ylo yhi + 0 50.0 zlo zhi +} + diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_run.sh b/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_run.sh new file mode 100755 index 0000000000..cf51fa8705 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_run.sh @@ -0,0 +1,33 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.npt # minimization and simulation at constant pressure + +# or + +lmp_linux -i run.in.nvt # minimization and simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation are ignored when beginning the simulation at constant volume. +# This can be fixed. Read "run.in.nvt" for equilibration instructions.) + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.npt +# or +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_setup.sh new file mode 100755 index 0000000000..3a08212692 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_setup.sh @@ -0,0 +1,23 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -atomstyle full system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_visualize.txt new file mode 100644 index 0000000000..73358e55dc --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 500 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/images/ice_rect8_crystal_3x2x2_LR.jpg b/tools/moltemplate/examples/all_atom_examples/ice_crystal/images/ice_rect8_crystal_3x2x2_LR.jpg new file mode 100644 index 0000000000..2cdc08b312 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/ice_crystal/images/ice_rect8_crystal_3x2x2_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/spce.lt new file mode 100644 index 0000000000..2b550b6309 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/spce.lt @@ -0,0 +1,52 @@ +# file "spce.lt" +# +# H1 H2 +# \ / +# O + +SPCE { + + write_once("In Init") { + # -- Default styles (for solo "SPCE" water) -- + units real + atom_style full + # (Hybrid force fields were not necessary but are used for portability.) + pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 + bond_style hybrid harmonic + angle_style hybrid harmonic + kspace_style pppm 0.0001 + pair_modify mix arithmetic + } + + write("Data Atoms") { + $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 + $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 + $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590 + } + + write_once("Data Masses") { + @atom:O 15.9994 + @atom:H 1.008 + } + + write("Data Bonds") { + $bond:OH1 @bond:OH $atom:O $atom:H1 + $bond:OH2 @bond:OH $atom:O $atom:H2 + } + + write("Data Angles") { + $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 + } + + write_once("In Settings") { + bond_coeff @bond:OH harmonic 1000.0 1.0 + angle_coeff @angle:HOH harmonic 1000.0 109.47 + pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 + pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058 + group spce type @atom:O @atom:H + fix fSHAKE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH + # (Remember to "unfix" fSHAKE during minimization.) + } + +} # end of definition of "SPCE" water molecule type + diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/spce_ice_rect8.lt b/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/spce_ice_rect8.lt new file mode 100644 index 0000000000..ccfd2f18c6 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/spce_ice_rect8.lt @@ -0,0 +1,57 @@ +# This ice (1h) unit cell is rectangular and contains 8 water molecules. +# (Coordinates and cell dimensions converted were from a PDB file.) +# The dimensions of the unit cell (in Angstroms) are: 4.521 7.832 7.362 + + +import "spce.lt" # <-- define the "SPCE" molecule + +SpceIceRect8 { + + # Create a 3-dimensional array of 8 water molecules + + wat = new SPCE[2][2][2] + + # Array indices will be correlated with position [xindex][yindex][zindex] + + # You can overwrite coordinates of atoms after they were created this way: + # (Order is not important) + # atom-ID molecule-ID atomType charge newX newY newZ + + write("Data Atoms") { + $atom:wat[1][0][0]/O $mol:wat[1][0][0] @atom:SPCE/O -0.8476 3.391 1.305 1.381 + $atom:wat[1][0][0]/H1 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 3.391 0.370 1.710 + $atom:wat[1][0][0]/H2 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 2.582 1.772 1.710 + $atom:wat[1][0][1]/O $mol:wat[1][0][1] @atom:SPCE/O -0.8476 3.391 1.305 5.981 + $atom:wat[1][0][1]/H1 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 3.391 1.305 6.970 + $atom:wat[1][0][1]/H2 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 4.200 1.772 5.652 + $atom:wat[0][0][0]/O $mol:wat[0][0][0] @atom:SPCE/O -0.8476 1.131 2.611 2.300 + $atom:wat[0][0][0]/H1 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 1.131 2.611 3.289 + $atom:wat[0][0][0]/H2 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 0.320 2.143 1.971 + $atom:wat[0][0][1]/O $mol:wat[0][0][1] @atom:SPCE/O -0.8476 1.131 2.611 5.061 + $atom:wat[0][0][1]/H1 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.940 2.143 5.391 + $atom:wat[0][0][1]/H2 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.131 3.546 5.391 + $atom:wat[0][1][0]/O $mol:wat[0][1][0] @atom:SPCE/O -0.8476 1.131 5.221 1.381 + $atom:wat[0][1][0]/H1 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.131 4.286 1.710 + $atom:wat[0][1][0]/H2 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 0.320 5.688 1.710 + $atom:wat[0][1][1]/O $mol:wat[0][1][1] @atom:SPCE/O -0.8476 1.131 5.221 5.981 + $atom:wat[0][1][1]/H1 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.131 5.221 6.970 + $atom:wat[0][1][1]/H2 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.940 5.688 5.652 + $atom:wat[1][1][0]/O $mol:wat[1][1][0] @atom:SPCE/O -0.8476 3.391 6.526 2.300 + $atom:wat[1][1][0]/H1 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 3.391 6.526 3.289 + $atom:wat[1][1][0]/H2 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 2.582 6.058 1.971 + $atom:wat[1][1][1]/O $mol:wat[1][1][1] @atom:SPCE/O -0.8476 3.391 6.526 5.061 + $atom:wat[1][1][1]/H1 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 4.200 6.058 5.391 + $atom:wat[1][1][1]/H2 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 3.391 7.462 5.391 + } +} # IceRect8 + +# Credit goes to Martin Chaplin. +# These coordinates were orignally downloaded from Martin Chaplin's +# website: http://www.btinternet.com/~martin.chaplin/ice1h.html +# ... and then they were stretched independently in the xy and z +# directions in order to match the lattice parameters measured by +# Rottger et al., +# "Lattice constants and thermal expansion of H2O and D2O ice Ih" +# between 10 and 265K", Acta Crystallogr. B, 50 (1994) 644-648 +# I am using the lattice constants measured at temperature 265K +# (and pressure=100Torr). diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/system.lt new file mode 100644 index 0000000000..b4f22f9dcf --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/system.lt @@ -0,0 +1,11 @@ +import "spce_ice_rect8.lt" + +cells = new SpceIceRect8 [3].move(4.521, 0.0, 0.0) + [2].move( 0.0, 7.832, 0.0) + [2].move( 0.0, 0.0, 7.362) + +write_once("Data Boundary") { + 0 13.563 xlo xhi + 0 15.664 ylo yhi + 0 14.724 zlo zhi +} diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/run.in.npt b/tools/moltemplate/examples/all_atom_examples/ice_crystal/run.in.npt new file mode 100644 index 0000000000..2bf2e0c03f --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/ice_crystal/run.in.npt @@ -0,0 +1,38 @@ +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + + +# -- minimization protocol -- + +# Note: The minimization step is not necessary in this example. However +# in general, it's always a good idea to minimize the system beforehand. +# fSHAKE was defined in system.in.settings. It is incompatible with "minimize". +unfix fSHAKE +minimize 1.0e-5 1.0e-7 100000 400000 +# Now read "system.in.settings" in order to redefine fSHAKE again: +include system.in.settings + +# -- simulation protocol -- + + +timestep 2.0 +dump 1 all custom 200 traj_npt.lammpstrj id mol type x y z ix iy iz +fix fxnpt all npt temp 400.0 400.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 + +thermo 100 +#thermo_modify flush yes + +run 20000 + +write_restart system_after_npt.rst diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/ice_crystal/run.in.nvt new file mode 100644 index 0000000000..b23a288c47 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/ice_crystal/run.in.nvt @@ -0,0 +1,61 @@ +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + + +# Normally, I would minimize the system and equilibrate the system at constant +# pressure and temperature beforehand. If you run lammps with "run.in.npt", +# it will generate a restart file "system_after_npt.rst" with reasonable +# coordinates at that temperature and pressure. Then we could load it now: +# +#read_restart system_after_npt.rst +# +# Unfortunately the LAMMPS "read_restart" command has been undependable over +# the past year (2012), and I feel it is safer to remove it from the examples. +# Instead, for this example, I just read the raw coordinates generated by +# moltemplate (and the default volume). (I get fewer questions this way.) +# However you should never run any liquid simulations at constant volume without +# pressure equilibration first. Hopefully in the future "read_restart" will +# work. Until then, try "read_dump", "dump2data.py", or "restart2data". + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + + +# -- minimization protocol -- + +# Note: The minimization step is not necessary in this example. However +# in general, it's always a good idea to minimize the system beforehand. +# fSHAKE was defined in system.in.settings. It is incompatible with "minimize". +unfix fSHAKE +minimize 1.0e-5 1.0e-7 100000 400000 +# Now read "system.in.settings" in order to redefine fSHAKE again: +include system.in.settings + +# -- simulation protocol -- + + + +timestep 2.0 +dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz +fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 + + +thermo 500 +#thermo_modify flush yes + + +#restart 100000 restart_nvt + +run 50000 + +write_restart system_after_nvt.rst + + diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/README.TXT b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README.TXT new file mode 100644 index 0000000000..83b4ad80bf --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README.TXT @@ -0,0 +1,51 @@ +This is a small version of a carbon-nanotube, water capillary system. +It was inspired by this paper: + + Laurent Joly, J. Chem. Phys. 135(21):214705 (2011) + +-------- Requirements: ------- +To run this system at constant pressure, it might help to compile LAMMPS +with the optional RIGID package, and use "fix rigid" on the carbon. +(The use of fix rigid is controversial.) Running at NVT does not require this. +------------------------------ + +Note: To investigate the behavior from that paper, it might be a good + idea to increase the size of the water reservoir, the spacing between + the walls, and the size of the system in the X and Y directions. + +Note: Explicit carbon-carbon bonds: + In the graphene and nanotube structures, I did not try to connect the + carbon atoms together with bonds. Instead we will hold these structures + rigid by not integrating their equations of motion. + (If you want to simulate movement of the carbon atoms at high + temperatures or tension, LAMMPS has 3-body/many-body LAMMPS force-fields + available for simulating the behaviour of carbon in graphite. I know + that you don't need to specify bonds to use these force fields. I do + not know know if these force fields work for nanotubes or graphene.) + +Note: Other modeling tools: + If you need explicit bonds between carbon atoms, then you must add them + yourself or use a different tool. Currently (2012-10-20), moltemplate does + not generate bonds automatically. The "Nanotube Builder" and "topotools" + plugins for for VMD can generate a nanotube with bonds in LAMMPS data + format. You can then convert this data file to .LT format using the + ltemplify.py utility and then import it into another .LT file and play + with it later. (In the "cnad-cnt" example, the carbon nanotube was built + using "Nanotube Builder" and topotools, and processed with ltemplify.py) + + +# WARNING: THIS IS NOT A REALISTIC MODEL OF A GRAPHENE-NANOTUBE JUNCTION. +# A real junction would be curved and deformed near the boundary, +# (not 90 degrees) and it would not be built entirely from hexagons. +# (This is not a problem in this example because the carbon atoms +# are immobilized.) If you want to simulate the behavior of +# real graphene or nanotube junctions, you must be more careful. +# To solve this problem: +# Moltemplate allows you to move, customize or delete individual +# atoms near the boundary. You can move atoms by overwriting their +# coordinates using additional write("Data Atoms") statements (after +# the walls and tube are created). You can also change their charge. +# Alternately, you could start with the structure provided here, and +# relax/minimize the coordinates of the carbon atoms using LAMMPS +# before using it in other simulations. +# Or you could do both (customization & minimization). diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_run.sh b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_run.sh new file mode 100755 index 0000000000..8a470b9551 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_run.sh @@ -0,0 +1,24 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.nvt # minimization and simulation at constant volume +lmp_linux -i run.in.npt # minimization and simulation at constant pressure + # (WARNING: The "run.in.npt" example has not been + # rigorously tested and may fail.) + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.npt +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_setup.sh new file mode 100755 index 0000000000..acc5fbbaad --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_setup.sh @@ -0,0 +1,23 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_visualize.txt new file mode 100644 index 0000000000..206db99038 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_visualize.txt @@ -0,0 +1,77 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + To shift the box by a fraction in the x direction (for example) + do this: + + pbc wrap -compound res -all -shiftcenterrel {-0.50 -0.52 0.0 } + pbc box -shiftcenterrel {-0.50 -0.52 0.0 } + + # Alternately if you have a solute whose atoms are all of type 1, + # then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/all_atom_examples/nanotube+water/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 0000000000..bf019b4c31 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,3195 @@ +PSF + + 1 !NTITLE + REMARKS VMD-generated NAMD/X-Plor PSF structure file + + 2454 !NATOM + 1 1 1 1 0.000000 12.0000 0 + 2 1 1 1 0.000000 12.0000 0 + 3 2 1 1 0.000000 12.0000 0 + 4 2 1 1 0.000000 12.0000 0 + 5 3 1 1 0.000000 12.0000 0 + 6 3 1 1 0.000000 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b/tools/moltemplate/examples/all_atom_examples/nanotube+water/images/water_side_nopbc_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/README.sh b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/README.sh new file mode 100644 index 0000000000..8b16c87e3f --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/README.sh @@ -0,0 +1,27 @@ +# This is a small version of a carbon-nanotube, water capillary system. +# It was inspired by this paper: +# +# Laurent Joly, J. Chem. Phys. 135(21):214705 (2011) +# +# Note: To investigate the behavior from that paper, you would have to increase +# the spacing between the two graphene sheets to prevent the water from +# making contact with the lower graphene wall. +# +# Requirements: 1) Set your $MOLTEMPLATE_PATH variable +# 2) The "RIGID" LAMMPS package may be needed later +# To run this system at constant pressure, it might help to compile LAMMPS with +# the optional RIGID package, and use "fix rigid" on the carbon. (Optional.) +# +# Also, if you have not yet done this set your MOLTEMPLATE_PATH environment +# variable to access it. (See installation instructions.) +# Most likely some of the files in this example (like graphene.lt, tip3p2004.lt) +# are not in this directory, but are in the "common" directory. +# Set MOLTEMPLATE_PATH to point to the "common" directory. +# +# ----------------------------------------------------------- +# +# To run moltemplate, use: + +moltemplate.sh system.lt + +# This will generate:system.data, system.in, system.in.init, system.in.settings diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene.lt new file mode 100644 index 0000000000..9122dc1376 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene.lt @@ -0,0 +1,107 @@ +# This file contains a unit cell for building graphene and nanotubes +# +# +# The 2AtomCellAlignX "molecule" defined below is a minimal unit cell for any +# hexagonal tesselation in 2-dimensions. (See "graphene_unit_cell.jpg") +# Surfaces constructed with this unit cell can be flat or curved into tubes. +# The distance between nearest-neighbor carbon atoms (ie the length of a +# carbon-carbon bond) is equal to "d" which I set to 1.42 Angstroms. +# +# d = length of each hexagon's side = 1.42 Angstroms +# L = length of each hexagon = 2*d = 2.84 Angstroms +# W = width of each hexagon = 2*d*sqrt(3)/2 = 2.4595121467478056 Angstroms +# w = width of hexagon rows = 1.5*l = 2.13 Angstroms +# +# Consequently, the Lattice-cell vectors for singe-layer graphene are: +# (2.4595121467478, 0, 0) (aligned with X axis) +# (1.2297560733739, 2.13, 0) (2.13 = 1.5*d) +# So, to build a sheet of graphite, you could use: +# sheet = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0) +# [10].move(1.2297560733739,2.13,0) + + + + +Graphene { + + 2AtomCellAlignX + { + # atomID molID atomType charge x y z + write("Data Atoms") { + $atom:C1 $mol:... @atom:../C 0.0 -0.61487803668695 -0.355 0.0 + $atom:C2 $mol:... @atom:../C 0.0 0.61487803668695 0.355 0.0 + } + } + + # Now define properties of the Carbon graphene atom + + write_once("In Init") { + pair_style hybrid lj/charmm/coul/charmm 9.0 10.0 + } + + write_once("Data Masses") { + @atom:C 12.0 + } + + write_once("In Settings") { + # i j epsilon sigma + pair_coeff @atom:C @atom:C lj/charmm/coul/charmm 0.068443 3.407 + + # These Lennard-Jones parameters come from + # R. Saito, R. Matsuo, T. Kimura, G. Dresselhaus, M.S. Dresselhaus, + # Chem Phys Lett, 348:187 (2001) + + # Define a group consisting of only carbon atoms in graphene molecules + group Cgraphene type @atom:C + } + + # Notice that the two atoms in the unit-cell above lie in the XY plane. + # (Their z-coordinate is zero). It's also useful to have a version of + # this object which lies in the XZ plan. So we define this below: + + 2AtomCellAlignXZ = 2AtomCellAlignX.rot(90,1,0,0) + +} # Graphene + + + + + + + + + + +# ------------ Graphite ----------- +# +# Note: For graphite: sheets stacked in the Z direction are separated by a +# distance of 3.35 Angstroms, and shifted in an alternating +/-Y direction +# by a distance of d (1.42 Angstroms). To add additional graphene layers +# you could use: +# sheet2 = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0) +# [10].move(1.2297560733739,2.13,0) +# sheet2[*][*].move(0, 1.42, 3.35) +# sheet3 = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0) +# [10].move(1.2297560733739,2.13,0) +# sheet3[*][*].move(0, -1.42, 6.70) +# etc... +# However, to build a thick sheet of graphite, it would +# be more efficient to use a 4-atom unit cell: +# +#Graphene { +# GraphiteCell { +# # atomID molID atomType charge x y z +# write("Data Atoms") { +# $atom:C1 $mol:... @atom:../C 0.0 -0.61487803668695 -0.355 0.0 +# $atom:C2 $mol:... @atom:../C 0.0 0.61487803668695 0.355 0.0 +# $atom:C3 $mol:... @atom:../C 0.0 -0.61487803668695 1.065 3.35 +# $atom:C4 $mol:... @atom:../C 0.0 0.61487803668695 1.775 3.35 +# } +# } # GraphiteCell +#} +# +# Then you could create a thick sheet of graphite this way: +# +# graphite = new Graphene/GraphiteCell [10].move(2.4595121467478,0,0) +# [10].move(1.2297560733739,2.13,0) +# [5].move(0,0,6.70) diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene_walls.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene_walls.lt new file mode 100644 index 0000000000..53499334de --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene_walls.lt @@ -0,0 +1,54 @@ + +import "graphene.lt" + +# -------------- graphene sheet ----------------- + +# Notes: +# Hexagonal lattice with: +# d = length of each hexagonal side = 1.42 Angstroms +# L = length of each hexagon = 2*d = 2.84 Angstroms +# W = width of each hexagon = 2*d*sqrt(3)/2 = 2.4595121467478 Angstroms +# w = width of hexagon rows = 1.5*d = 2.13 Angstroms + +Wall { + unitcells = new Graphene/2AtomCellAlignX [14].move(1.2297560733739, 2.13, 0) + [13].move(2.4595121467478, 0, 0) + unitcells[*][*].move(-24.595121467478, -14.91, 0.000) + + # Now cut a hole in the graphene sheet roughly where the nanotube is located + delete unitcells[5][7-8] # delete 2 unit cells (2 atoms each, 4 atoms total) + delete unitcells[6][6-8] # delete 3 unit cells (2 atoms each, 6 atoms total) + delete unitcells[7][5-8] # delete 4 unit cells (2 atoms each, 8 atoms total) + delete unitcells[8][5-7] # delete 3 unit cells (2 atoms each, 6 atoms total) + delete unitcells[9][5-6] # delete 2 unit cells (2 atoms each, 4 atoms total) + # Optional fine tuning: delete a few additional atoms around the edges + delete unitcells[5][6]/C2 # delete a single atom + delete unitcells[6][5]/C2 # delete a single atom + delete unitcells[6][9]/C1 # delete a single atom + delete unitcells[8][4]/C2 # delete a single atom + delete unitcells[8][8]/C1 # delete a single atom + delete unitcells[9][7]/C1 # delete a single atom +} + +# Make two copies of the wall, and place them on either end of the nanotube + +wall1 = new Wall.move(0, 0, 32.0) +wall2 = new Wall.move(0, 0, 58.26) + + +# WARNING: A reader has emailed me to point out that: +# THIS IS NOT A REALISTIC MODEL OF A GRAPHENE-NANOTUBE JUNCTION. +# A real junction would be curved and deformed near the boundary, +# (not 90 degrees) and it would not be built entirely from hexagons. +# (This is not a problem in this example because the carbon atoms +# are immobilized.) If you want to simulate the behavior of +# real graphene or nanotube junctions, you must be more careful. +# To solve this problem: +# Moltemplate allows you to move, customize or delete individual +# atoms near the boundary. You can move atoms by overwriting their +# coordinates using additional write("Data Atoms") statements (after +# the walls and tube are created). You can also change their charge. +# Alternately, you could start with the structure provided here, and +# relax/minimize the coordinates of the carbon atoms using LAMMPS +# before using it in other simulations. +# Or you could do both (customization & minimization). diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/nanotube.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/nanotube.lt new file mode 100644 index 0000000000..02d7dd762d --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/nanotube.lt @@ -0,0 +1,24 @@ +import "graphene.lt" + +# ------------------ nanotube --------------- + +# Now use this to build a simple ("zigzag") nanotube where the long-axis of each +# hexagon is aligned with the tube axis (along the Z direction). If the +# cicumference of a "zigzag" nanotube contains N hexagons, then the radius of +# the tube, R=(W/4)/tan((2*pi)/(4*N)), where W=2*d*sqrt(3)/2, and d = the carbon +# bond length. If N=14 and d=1.42 Ansgroms then R=5.457193512764 Angstroms +# In the Joly 2011 paper, the tube radii varied between 5.14 and 18.7 Angstroms. + + +nanotube = new Graphene/2AtomCellAlignXZ.move(0, 5.457193512764, 0) # 5.45 = R + [14].rot(25.7142857,0,0,1) #25.7=360/14 + [12].rot(12.8571429,0,0,1).move(0, 0, 2.13) #12.9=180/14 + #2.13= d*1.5 + + # Note: The length is 12 hexegons, the circumference is + # 14 hexegons (~=25.56 and 34.43 Angstroms, respectively). + +# Move all of the unit-cells in the nanotube between the two graphene sheets. + +nanotube[*][*].move(0, 0, 33.42) + diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/spce.lt new file mode 100644 index 0000000000..3bb7bca40a --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/spce.lt @@ -0,0 +1,52 @@ +# file "spce.lt" +# +# H1 H2 +# \ / +# O + +SPCE { + + write_once("In Init") { + # -- Default styles (for solo "SPCE" water) -- + units real + atom_style full + # (Hybrid force fields were not necessary but are used for portability.) + pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 + bond_style hybrid harmonic + angle_style hybrid harmonic + kspace_style pppm 0.0001 + pair_modify mix arithmetic + } + + write("Data Atoms") { + $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 + $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 + $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590 + } + + write_once("Data Masses") { + @atom:O 15.9994 + @atom:H 1.008 + } + + write("Data Bonds") { + $bond:OH1 @bond:OH $atom:O $atom:H1 + $bond:OH2 @bond:OH $atom:O $atom:H2 + } + + write("Data Angles") { + $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 + } + + write_once("In Settings") { + bond_coeff @bond:OH harmonic 200.0 1.0 + angle_coeff @angle:HOH harmonic 200.0 109.47 + pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 + pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058 + group spce type @atom:O @atom:H + fix fSHAKE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH + # (Remember to "unfix" fSHAKE during minimization.) + } + +} # end of definition of "SPCE" water molecule type + diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/system.lt new file mode 100644 index 0000000000..d46057fafd --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/system.lt @@ -0,0 +1,38 @@ +# This is a small version of a carbon-nanotube, water capillary system. It was +# inspired by this paper: Laurent Joly, J. Chem. Phys. 135(21):214705 (2011) + +import "graphene_walls.lt" + +import "nanotube.lt" + +import "water_box.lt" + + +# ------------ boundary conditions ------------ + +write_once("Data Boundary") { + -15.98682895386 15.98682895386 xlo xhi + -14.91 14.91 ylo yhi + 0.0 80.00 zlo zhi +} + +# --------------------------------------------- + + + +write_once("In Init") { + # -- override any earlier pair_style settings: -- + pair_style hybrid lj/charmm/coul/long 10.0 10.5 10.5 & + lj/charmm/coul/charmm 9.0 10.0 +} + + +write_once("In Settings") { + # --- We must eventually specify the interactions between the atoms --- + # --- in different molecule types (graphene-water interactions). --- + # (See Laurent Joly, J. Chem. Phys. 135(21):214705 (2011) for details + + pair_coeff @atom:Graphene/C @atom:SPCE/O lj/charmm/coul/long 0.114 3.28 + pair_coeff @atom:Graphene/C @atom:SPCE/H lj/charmm/coul/long 0.0 3.28 +} + diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/water_box.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/water_box.lt new file mode 100644 index 0000000000..c825276f5a --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/water_box.lt @@ -0,0 +1,20 @@ +import "spce.lt" + +# --------------- water ------------------ + +# Create a rhombohedral box of water. (A rectangular box works also.) + +wat = new SPCE [9].move(3.5526287, 0, 0 ) + [9].move(1.77631435, 3.3133, 0 ) + [6].move( 0, 0, 3.45) + +# Optional: Center the water box at the origin. (Not really necessary.) + +wat[*][*][*].move(-23.9802437, -14.90985, 11.47) + +# --------------- Note: ----------------- +# The spacing between water molecules does not matter much as long as it is +# reasonable. (I adjusted the spacing try to insure that the waters are spread +# uniformly throughout the box. We do not want bubles to form if there are +# gaps near the XY periodic boundaries.) We will have to equilibrate it later. + diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.npt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.npt new file mode 100644 index 0000000000..608b4fa382 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.npt @@ -0,0 +1,98 @@ +# THIS EXAMPLE HAS NOT BEEN RIGOROUSLY TESTED. +# (This simulation may fail. +# However the "run.in.nvt" example in this directory should work.) +# +# Requirements: +# To run this system at constant pressure, it might help to compile LAMMPS with +# the optional RIGID package, and use "fix rigid" on the carbon. (Optional.) +# The use of fix rigid is controversial. This method is demonstrated below. + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + + +# Only the Cgraphene atoms are immobile. +group mobile subtract all Cgraphene + + +# Unfortunately you can not use the LAMMPS "minimize" command on this system +# because there is no way to immobilize the carbon graphene & nanotube atoms +# during minimization. Instead, we can use langevin dynamics with a large +# damping parameter and a small timestep. + +print "--------- beginning minimization (using fix langevin) ---------" + +timestep 0.1 +fix fxlan mobile langevin 1.0 1.0 100.0 48279 +fix fxnve mobile nve # <-- needed by fix langevin (see lammps documentation) +thermo 100 +run 2500 + +unfix fxlan +unfix fxnve + +# -- simulation protocol -- + +print "--------- beginning simulation (using fix nvt) ---------" + +timestep 0.5 +dump 1 all custom 1000 traj_npt.lammpstrj id mol type x y z ix iy iz + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo 1000 # time interval for printing out "thermo" data + + + + + +# ------------------------- NPT --------------------------- + +# Set temp=300K, pressure=100bar, and equilibrate volume only in the z direction + +fix fxMoveStuff mobile npt temp 300 300 100 z 100 100 1000.0 dilate mobile + +# ------ CONTROVERSIAL (see below): ------ + +fix Ffreezestuff Cgraphene rigid/npt single temp 300 300 100 z 100 100 1000.0 force * off off off torque * off off off dilate mobile + +# -- Alternate npt rigid method -- +# I'm not sure which way is more correct, however +# this also seems to behave in a reasonable-looking way: +#fix Ffreezestuff Cgraphene rigid single force * off off off torque * off off off +# +# The use of either "fix rigid" or "fix rigid/npt" to immobilize +# an object is somewhat controversial. Feel free to omit it. +#(Neither Trung or Steve Plimpton use rigid or rigid/npt for immobilizing +#molecules, but I noticed that at NPT, it does a better job of maintaining +# the correct volume. However "fix rigid" has changed since then (2011), +# so this may no longer be true. Please use this example with caution.) +# ---------------------------------------- + +# IMPORTANT for NPT: You must use "neigh_modify" to turn off calculation of the +# forces between immobilized atoms. +neigh_modify exclude group Cgraphene Cgraphene + +# The next two lines recalculate the temperature +# using only the mobile degrees of freedom: + +compute tempMobile mobile temp +compute pressMobile all pressure tempMobile + +thermo_style custom step c_tempMobile c_pressMobile temp press vol + +fix_modify fxMoveStuff temp tempMobile + +run 100000 + +write_restart system_after_npt.rst diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.nvt new file mode 100644 index 0000000000..f4fd0bbc15 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.nvt @@ -0,0 +1,71 @@ +# ----------------------------- Initialization Section -------------------- + +include system.in.init + + +# ----------------------------- Atom Definition Section ------------------- + +read_data system.data + + +# ----------------------------- Settings Section -------------------------- + +include system.in.settings + + +# ----------------------------- Run Section ------------------------------- + + + +# Optional: Improve efficiency by omitting the calcuation of interactions +# between immobile atoms. (Note: This is not optional under NPT conditions.) +neigh_modify exclude group Cgraphene Cgraphene + +# Only the Cgraphene atoms are immobile. +group mobile subtract all Cgraphene + + + +# -- minimization protocol -- + +# Unfortunately you can not use the LAMMPS "minimize" command on this system +# because there is no way to immobilize the carbon graphene & nanotube atoms +# during minimization. Instead, we can use langevin dynamics with a large +# damping parameter and a small timestep. + +print "--------- beginning minimization (using fix langevin) ---------" + +timestep 0.1 +fix fxlan mobile langevin 1.0 1.0 100.0 48279 +fix fxnve mobile nve # <-- needed by fix langevin (see lammps documentation) +thermo 100 +run 2500 + +unfix fxlan +unfix fxnve + +# -- simulation protocol -- + +print "--------- beginning simulation (using fix nvt) ---------" + +timestep 1.0 +dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz + +thermo_style custom step temp pe etotal press vol epair #ebond eangle edihed +thermo 500 # time interval for printing out "thermo" data + + +# Integrate the equations of motion: +fix fxMoveStuff mobile nvt temp 300.0 300.0 100.0 + +# The next two lines recalculate the temperature +# using only the mobile degrees of freedom: + +compute tempMobile mobile temp +fix_modify fxMoveStuff temp tempMobile + +restart 5000000 restart_nvt +run 10000000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README.TXT b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README.TXT new file mode 100644 index 0000000000..0e58ef44c7 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README.TXT @@ -0,0 +1,10 @@ +This is a simple system of 260 water molecules. + +In this example, the coordinates of the atoms are read from a PDB file +instead of being specified manually (as well as the boundary information). + +The PDB file was generated by the useful "solvate" utility which comes with VMD. +(To generate this file yourself, run VMD, click on the "Extensions" menu, +and select Modeling-->Add Solvation Box. +In this example, I made a box whose x,y,z dimensions were 16,24,24.) + diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh new file mode 100755 index 0000000000..022c53ce3b --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh @@ -0,0 +1,31 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.npt # minimization and simulation at constant pressure +lmp_linux -i run.in.nvt # minimization and simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation are ignored when beginning the simulation at constant volume. +# This can be fixed. Read "run.in.nvt" for equilibration instructions.) + + + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.npt +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_setup.sh new file mode 100755 index 0000000000..5d2be21331 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_setup.sh @@ -0,0 +1,32 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + +cd moltemplate_files/ # (The .lt input files are in this directory) + + moltemplate.sh -pdb solvate.pdb system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ + + +# +#This will prepare LAMMPS input files for a box of water +#(In this example, we are using the "SPC/E" water model.) +#The number of water molecules in the "wat = new SPCE [260]" command +#must equal the number of water molecules in the PDB file. +# +#Coordinates and boundary-box information is read from the .pdb file. +# +#You can also specify this information directly in the ttree file. +#See the comments section in "system.lt" for details. +# diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_visualize.txt new file mode 100644 index 0000000000..8063d535f8 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_visualize.txt @@ -0,0 +1,64 @@ + ------- Instructions to view a trajectory in VMD -------- + + ------- Disclaimer ------- + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + + (Note, at this point the image shown in the VMD graphics window may + not appear correct or incomplete. The coordinates of the atoms may + overlap if you asked moltemplate.sh to load your coordinates from + a PDB or XYZ file. + However, later after you have run a simulation, the trajectories + should appear reasonably correct when you load them in VMD using + the PSF file you just generated.) + + +Later, to Load a trajectory in VMD: + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it + +----- Wrap the coordinates to the unit cell + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Enter: + + DISCLAIMER: I'M NOT SURE THESE COMMANDS ARE CORRECT. + LOOKUP "pbctools" FOR DETAILS. + + pbc wrap -compound res -all + pbc box + + # If you have a solute of type 1, then use this: + #pbc wrap -sel type=1 -all -centersel type=2 -center com + +"1" corresponds to the "O" atom type +"2" corresponds to the "H" atom type + +3) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types: + +sed -e 's/ 1 1 / O O /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > system.psf + +(If you do this, I guess that you might have to use + "type=O" and "type=H" in step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/README.sh b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/README.sh new file mode 100755 index 0000000000..4ebc7b17a3 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/README.sh @@ -0,0 +1,11 @@ + +# Run moltemplate this way: + +moltemplate.sh -pdb solvate.pdb system.lt + + +# The PDB file was generated by the "solvate" utility which comes with VMD. +# (To generate this file yourself, run VMD, click on the "Extensions" menu, +# and select Modeling-->Add Solvation Box. +# In this example, I made a box whose x,y,z dimensions were 16,24,24.) + diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/solvate.pdb b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/solvate.pdb new file mode 100644 index 0000000000..0ed5103cbb --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/solvate.pdb @@ -0,0 +1,782 @@ +CRYST1 16.000 24.000 24.000 90.00 90.00 90.00 P 1 1 +ATOM 1 OH2 TIP3W 5 3.668 10.082 15.904 1.00 0.00 WT1 O +ATOM 2 H1 TIP3W 5 3.224 10.451 15.101 1.00 0.00 WT1 H +ATOM 3 H2 TIP3W 5 3.092 10.379 16.627 1.00 0.00 WT1 H +ATOM 4 OH2 TIP3W 7 6.033 4.876 20.891 1.00 0.00 WT1 O +ATOM 5 H1 TIP3W 7 6.078 5.224 21.798 1.00 0.00 WT1 H +ATOM 6 H2 TIP3W 7 6.592 4.088 20.961 1.00 0.00 WT1 H +ATOM 7 OH2 TIP3W 21 5.186 16.696 12.072 1.00 0.00 WT1 O +ATOM 8 H1 TIP3W 21 6.083 16.979 11.816 1.00 0.00 WT1 H +ATOM 9 H2 TIP3W 21 5.337 15.832 12.490 1.00 0.00 WT1 H +ATOM 10 OH2 TIP3W 29 8.324 13.811 21.332 1.00 0.00 WT1 O +ATOM 11 H1 TIP3W 29 8.633 13.348 22.112 1.00 0.00 WT1 H +ATOM 12 H2 TIP3W 29 8.506 13.116 20.645 1.00 0.00 WT1 H +ATOM 13 OH2 TIP3W 44 3.786 16.318 1.310 1.00 0.00 WT1 O +ATOM 14 H1 TIP3W 44 3.781 15.388 1.196 1.00 0.00 WT1 H +ATOM 15 H2 TIP3W 44 4.528 16.580 0.781 1.00 0.00 WT1 H +ATOM 16 OH2 TIP3W 46 6.205 6.991 18.442 1.00 0.00 WT1 O +ATOM 17 H1 TIP3W 46 6.782 7.347 19.152 1.00 0.00 WT1 H +ATOM 18 H2 TIP3W 46 5.309 7.062 18.800 1.00 0.00 WT1 H +ATOM 19 OH2 TIP3W 48 2.750 8.844 9.629 1.00 0.00 WT1 O +ATOM 20 H1 TIP3W 48 2.110 8.290 9.998 1.00 0.00 WT1 H +ATOM 21 H2 TIP3W 48 2.164 9.245 8.962 1.00 0.00 WT1 H +ATOM 22 OH2 TIP3W 52 3.935 16.195 22.109 1.00 0.00 WT1 O +ATOM 23 H1 TIP3W 52 4.870 16.034 21.985 1.00 0.00 WT1 H +ATOM 24 H2 TIP3W 52 3.655 15.367 22.581 1.00 0.00 WT1 H +ATOM 25 OH2 TIP3W 64 10.674 8.909 4.986 1.00 0.00 WT1 O +ATOM 26 H1 TIP3W 64 10.998 8.871 5.932 1.00 0.00 WT1 H +ATOM 27 H2 TIP3W 64 9.748 9.270 5.075 1.00 0.00 WT1 H +ATOM 28 OH2 TIP3W 67 0.002 5.667 14.591 1.00 0.00 WT1 O +ATOM 29 H1 TIP3W 67 0.483 5.990 13.830 1.00 0.00 WT1 H +ATOM 30 H2 TIP3W 67 0.608 5.781 15.347 1.00 0.00 WT1 H +ATOM 31 OH2 TIP3W 68 9.882 9.156 14.916 1.00 0.00 WT1 O +ATOM 32 H1 TIP3W 68 9.574 9.753 15.597 1.00 0.00 WT1 H +ATOM 33 H2 TIP3W 68 10.021 8.264 15.289 1.00 0.00 WT1 H +ATOM 34 OH2 TIP3W 87 1.661 6.681 1.943 1.00 0.00 WT1 O +ATOM 35 H1 TIP3W 87 1.943 5.739 1.981 1.00 0.00 WT1 H +ATOM 36 H2 TIP3W 87 0.778 6.599 1.483 1.00 0.00 WT1 H +ATOM 37 OH2 TIP3W 88 4.821 20.603 11.239 1.00 0.00 WT1 O +ATOM 38 H1 TIP3W 88 5.466 20.782 11.963 1.00 0.00 WT1 H +ATOM 39 H2 TIP3W 88 5.384 20.914 10.456 1.00 0.00 WT1 H +ATOM 40 OH2 TIP3W 90 15.022 20.855 12.831 1.00 0.00 WT1 O +ATOM 41 H1 TIP3W 90 14.222 20.809 13.292 1.00 0.00 WT1 H +ATOM 42 H2 TIP3W 90 14.673 21.057 11.918 1.00 0.00 WT1 H +ATOM 43 OH2 TIP3W 94 1.339 3.782 22.814 1.00 0.00 WT1 O +ATOM 44 H1 TIP3W 94 0.839 3.425 22.087 1.00 0.00 WT1 H +ATOM 45 H2 TIP3W 94 1.775 3.077 23.138 1.00 0.00 WT1 H +ATOM 46 OH2 TIP3W 95 0.485 15.137 22.476 1.00 0.00 WT1 O +ATOM 47 H1 TIP3W 95 0.644 15.425 23.349 1.00 0.00 WT1 H +ATOM 48 H2 TIP3W 95 0.312 15.961 21.975 1.00 0.00 WT1 H +ATOM 49 OH2 TIP3W 111 10.426 7.604 2.404 1.00 0.00 WT1 O +ATOM 50 H1 TIP3W 111 10.761 8.401 1.994 1.00 0.00 WT1 H +ATOM 51 H2 TIP3W 111 10.248 7.889 3.308 1.00 0.00 WT1 H +ATOM 52 OH2 TIP3W 113 4.269 22.752 16.265 1.00 0.00 WT1 O +ATOM 53 H1 TIP3W 113 4.149 23.680 15.888 1.00 0.00 WT1 H +ATOM 54 H2 TIP3W 113 5.061 22.796 16.776 1.00 0.00 WT1 H +ATOM 55 OH2 TIP3W 130 10.926 5.365 1.018 1.00 0.00 WT1 O +ATOM 56 H1 TIP3W 130 11.138 4.769 1.754 1.00 0.00 WT1 H +ATOM 57 H2 TIP3W 130 10.657 6.212 1.493 1.00 0.00 WT1 H +ATOM 58 OH2 TIP3W 133 8.647 4.314 19.278 1.00 0.00 WT1 O +ATOM 59 H1 TIP3W 133 7.964 3.611 19.326 1.00 0.00 WT1 H +ATOM 60 H2 TIP3W 133 8.043 5.064 19.153 1.00 0.00 WT1 H +ATOM 61 OH2 TIP3W 134 8.381 17.319 23.275 1.00 0.00 WT1 O +ATOM 62 H1 TIP3W 134 7.516 17.340 23.695 1.00 0.00 WT1 H +ATOM 63 H2 TIP3W 134 8.431 18.263 23.009 1.00 0.00 WT1 H +ATOM 64 OH2 TIP3W 150 4.299 17.774 7.169 1.00 0.00 WT1 O +ATOM 65 H1 TIP3W 150 3.303 17.803 7.322 1.00 0.00 WT1 H +ATOM 66 H2 TIP3W 150 4.533 18.755 6.924 1.00 0.00 WT1 H +ATOM 67 OH2 TIP3W 152 8.892 12.977 5.321 1.00 0.00 WT1 O +ATOM 68 H1 TIP3W 152 8.119 12.478 5.443 1.00 0.00 WT1 H +ATOM 69 H2 TIP3W 152 9.342 12.557 4.536 1.00 0.00 WT1 H +ATOM 70 OH2 TIP3W 167 2.174 18.468 2.212 1.00 0.00 WT1 O +ATOM 71 H1 TIP3W 167 2.632 17.628 2.203 1.00 0.00 WT1 H +ATOM 72 H2 TIP3W 167 2.931 19.120 2.281 1.00 0.00 WT1 H +ATOM 73 OH2 TIP3W 239 13.612 17.680 18.622 1.00 0.00 WT1 O +ATOM 74 H1 TIP3W 239 13.744 17.414 19.508 1.00 0.00 WT1 H +ATOM 75 H2 TIP3W 239 14.526 17.831 18.347 1.00 0.00 WT1 H +ATOM 76 OH2 TIP3W 443 9.935 12.876 10.191 1.00 0.00 WT1 O +ATOM 77 H1 TIP3W 443 9.709 12.098 9.634 1.00 0.00 WT1 H +ATOM 78 H2 TIP3W 443 9.472 12.766 11.018 1.00 0.00 WT1 H +ATOM 79 OH2 TIP3W 450 7.060 2.074 19.830 1.00 0.00 WT1 O +ATOM 80 H1 TIP3W 450 7.650 1.619 20.528 1.00 0.00 WT1 H +ATOM 81 H2 TIP3W 450 6.148 1.796 20.035 1.00 0.00 WT1 H +ATOM 82 OH2 TIP3W 465 13.891 1.919 2.992 1.00 0.00 WT1 O +ATOM 83 H1 TIP3W 465 14.198 2.681 3.422 1.00 0.00 WT1 H +ATOM 84 H2 TIP3W 465 13.212 1.577 3.578 1.00 0.00 WT1 H +ATOM 85 OH2 TIP3W 466 8.823 10.581 8.827 1.00 0.00 WT1 O +ATOM 86 H1 TIP3W 466 8.183 10.753 8.148 1.00 0.00 WT1 H +ATOM 87 H2 TIP3W 466 8.389 10.061 9.534 1.00 0.00 WT1 H +ATOM 88 OH2 TIP3W 469 9.078 11.967 12.734 1.00 0.00 WT1 O +ATOM 89 H1 TIP3W 469 8.228 11.561 12.993 1.00 0.00 WT1 H +ATOM 90 H2 TIP3W 469 9.512 12.194 13.560 1.00 0.00 WT1 H +ATOM 91 OH2 TIP3W 484 10.282 0.640 2.053 1.00 0.00 WT1 O +ATOM 92 H1 TIP3W 484 10.367 0.959 3.016 1.00 0.00 WT1 H +ATOM 93 H2 TIP3W 484 9.743 1.323 1.667 1.00 0.00 WT1 H +ATOM 94 OH2 TIP3W 485 4.618 8.125 7.777 1.00 0.00 WT1 O +ATOM 95 H1 TIP3W 485 5.405 7.919 8.314 1.00 0.00 WT1 H +ATOM 96 H2 TIP3W 485 4.002 8.458 8.422 1.00 0.00 WT1 H +ATOM 97 OH2 TIP3W 486 3.403 4.687 9.815 1.00 0.00 WT1 O +ATOM 98 H1 TIP3W 486 3.109 5.272 9.097 1.00 0.00 WT1 H +ATOM 99 H2 TIP3W 486 3.817 3.973 9.327 1.00 0.00 WT1 H +ATOM 100 OH2 TIP3W 489 3.276 7.465 19.325 1.00 0.00 WT1 O +ATOM 101 H1 TIP3W 489 2.772 6.991 19.964 1.00 0.00 WT1 H +ATOM 102 H2 TIP3W 489 3.604 8.288 19.753 1.00 0.00 WT1 H +ATOM 103 OH2 TIP3W 503 3.119 10.325 13.158 1.00 0.00 WT1 O +ATOM 104 H1 TIP3W 503 3.598 10.900 12.512 1.00 0.00 WT1 H +ATOM 105 H2 TIP3W 503 3.440 9.430 12.962 1.00 0.00 WT1 H +ATOM 106 OH2 TIP3W 506 2.378 5.806 16.253 1.00 0.00 WT1 O +ATOM 107 H1 TIP3W 506 2.157 6.161 17.099 1.00 0.00 WT1 H +ATOM 108 H2 TIP3W 506 3.301 6.032 16.126 1.00 0.00 WT1 H +ATOM 109 OH2 TIP3W 507 6.382 22.271 2.319 1.00 0.00 WT1 O +ATOM 110 H1 TIP3W 507 5.550 22.035 1.847 1.00 0.00 WT1 H +ATOM 111 H2 TIP3W 507 6.859 21.472 2.192 1.00 0.00 WT1 H +ATOM 112 OH2 TIP3W 509 4.017 3.905 19.418 1.00 0.00 WT1 O +ATOM 113 H1 TIP3W 509 3.142 4.042 19.132 1.00 0.00 WT1 H +ATOM 114 H2 TIP3W 509 4.582 4.727 19.295 1.00 0.00 WT1 H +ATOM 115 OH2 TIP3W 511 2.344 20.472 21.631 1.00 0.00 WT1 O +ATOM 116 H1 TIP3W 511 2.932 20.821 20.945 1.00 0.00 WT1 H +ATOM 117 H2 TIP3W 511 1.467 20.548 21.138 1.00 0.00 WT1 H +ATOM 118 OH2 TIP3W 517 14.526 10.532 20.137 1.00 0.00 WT1 O +ATOM 119 H1 TIP3W 517 14.162 9.733 20.503 1.00 0.00 WT1 H +ATOM 120 H2 TIP3W 517 14.466 10.420 19.194 1.00 0.00 WT1 H +ATOM 121 OH2 TIP3W 533 5.573 14.804 19.090 1.00 0.00 WT1 O +ATOM 122 H1 TIP3W 533 5.959 15.339 19.808 1.00 0.00 WT1 H +ATOM 123 H2 TIP3W 533 5.869 15.413 18.331 1.00 0.00 WT1 H +ATOM 124 OH2 TIP3W 543 5.458 13.097 4.589 1.00 0.00 WT1 O +ATOM 125 H1 TIP3W 543 5.673 13.019 3.612 1.00 0.00 WT1 H +ATOM 126 H2 TIP3W 543 4.899 13.894 4.657 1.00 0.00 WT1 H +ATOM 127 OH2 TIP3W 550 4.552 1.370 20.330 1.00 0.00 WT1 O +ATOM 128 H1 TIP3W 550 4.274 2.194 19.953 1.00 0.00 WT1 H +ATOM 129 H2 TIP3W 550 4.235 0.801 19.571 1.00 0.00 WT1 H +ATOM 130 OH2 TIP3W 554 5.160 13.744 7.954 1.00 0.00 WT1 O +ATOM 131 H1 TIP3W 554 6.048 13.422 8.207 1.00 0.00 WT1 H +ATOM 132 H2 TIP3W 554 5.008 14.493 8.528 1.00 0.00 WT1 H +ATOM 133 OH2 TIP3W 558 10.390 6.386 18.828 1.00 0.00 WT1 O +ATOM 134 H1 TIP3W 558 10.688 6.484 19.731 1.00 0.00 WT1 H +ATOM 135 H2 TIP3W 558 9.844 5.589 18.921 1.00 0.00 WT1 H +ATOM 136 OH2 TIP3W 562 1.678 21.942 1.035 1.00 0.00 WT1 O +ATOM 137 H1 TIP3W 562 1.272 21.280 1.592 1.00 0.00 WT1 H +ATOM 138 H2 TIP3W 562 1.498 22.809 1.493 1.00 0.00 WT1 H +ATOM 139 OH2 TIP3W 568 9.630 21.547 3.000 1.00 0.00 WT1 O +ATOM 140 H1 TIP3W 568 9.601 22.471 2.643 1.00 0.00 WT1 H +ATOM 141 H2 TIP3W 568 9.287 20.954 2.312 1.00 0.00 WT1 H +ATOM 142 OH2 TIP3W 575 2.344 10.571 2.624 1.00 0.00 WT1 O +ATOM 143 H1 TIP3W 575 2.122 10.753 3.553 1.00 0.00 WT1 H +ATOM 144 H2 TIP3W 575 2.947 9.791 2.617 1.00 0.00 WT1 H +ATOM 145 OH2 TIP3W 584 0.823 23.668 2.888 1.00 0.00 WT1 O +ATOM 146 H1 TIP3W 584 1.636 23.316 3.340 1.00 0.00 WT1 H +ATOM 147 H2 TIP3W 584 0.253 23.978 3.640 1.00 0.00 WT1 H +ATOM 148 OH2 TIP3W 594 2.710 6.185 7.540 1.00 0.00 WT1 O +ATOM 149 H1 TIP3W 594 2.467 6.236 6.561 1.00 0.00 WT1 H +ATOM 150 H2 TIP3W 594 3.410 6.855 7.580 1.00 0.00 WT1 H +ATOM 151 OH2 TIP3W 595 6.911 19.458 17.335 1.00 0.00 WT1 O +ATOM 152 H1 TIP3W 595 7.517 20.118 16.957 1.00 0.00 WT1 H +ATOM 153 H2 TIP3W 595 6.315 19.136 16.588 1.00 0.00 WT1 H +ATOM 154 OH2 TIP3W 613 13.540 22.220 2.748 1.00 0.00 WT1 O +ATOM 155 H1 TIP3W 613 12.965 22.475 3.462 1.00 0.00 WT1 H +ATOM 156 H2 TIP3W 613 14.428 22.404 3.074 1.00 0.00 WT1 H +ATOM 157 OH2 TIP3W 634 10.929 14.750 5.718 1.00 0.00 WT1 O +ATOM 158 H1 TIP3W 634 10.050 14.541 5.408 1.00 0.00 WT1 H +ATOM 159 H2 TIP3W 634 11.401 13.879 5.717 1.00 0.00 WT1 H +ATOM 160 OH2 TIP3W 822 0.747 4.469 10.579 1.00 0.00 WT1 O +ATOM 161 H1 TIP3W 822 0.426 3.568 10.339 1.00 0.00 WT1 H +ATOM 162 H2 TIP3W 822 1.505 4.585 9.990 1.00 0.00 WT1 H +ATOM 163 OH2 TIP3W 849 5.356 5.388 16.046 1.00 0.00 WT1 O +ATOM 164 H1 TIP3W 849 5.884 6.064 16.461 1.00 0.00 WT1 H +ATOM 165 H2 TIP3W 849 5.592 4.622 16.537 1.00 0.00 WT1 H +ATOM 166 OH2 TIP3W 867 10.704 6.721 15.883 1.00 0.00 WT1 O +ATOM 167 H1 TIP3W 867 10.901 6.912 16.836 1.00 0.00 WT1 H +ATOM 168 H2 TIP3W 867 10.127 5.972 15.998 1.00 0.00 WT1 H +ATOM 169 OH2 TIP3W 891 11.763 19.614 9.958 1.00 0.00 WT1 O +ATOM 170 H1 TIP3W 891 12.279 20.405 9.866 1.00 0.00 WT1 H +ATOM 171 H2 TIP3W 891 12.435 18.905 9.901 1.00 0.00 WT1 H +ATOM 172 OH2 TIP3W 906 7.027 2.224 13.411 1.00 0.00 WT1 O +ATOM 173 H1 TIP3W 906 6.185 2.801 13.535 1.00 0.00 WT1 H +ATOM 174 H2 TIP3W 906 6.692 1.403 13.742 1.00 0.00 WT1 H +ATOM 175 OH2 TIP3W 908 4.028 7.699 12.776 1.00 0.00 WT1 O +ATOM 176 H1 TIP3W 908 4.577 7.193 12.138 1.00 0.00 WT1 H +ATOM 177 H2 TIP3W 908 3.171 7.320 12.544 1.00 0.00 WT1 H +ATOM 178 OH2 TIP3W 924 12.493 9.451 2.215 1.00 0.00 WT1 O +ATOM 179 H1 TIP3W 924 12.908 9.840 2.987 1.00 0.00 WT1 H +ATOM 180 H2 TIP3W 924 12.982 8.641 2.039 1.00 0.00 WT1 H +ATOM 181 OH2 TIP3W 927 11.177 9.610 7.928 1.00 0.00 WT1 O +ATOM 182 H1 TIP3W 927 10.443 10.172 8.053 1.00 0.00 WT1 H +ATOM 183 H2 TIP3W 927 10.866 8.788 8.298 1.00 0.00 WT1 H +ATOM 184 OH2 TIP3W 928 1.838 3.206 15.398 1.00 0.00 WT1 O +ATOM 185 H1 TIP3W 928 2.201 4.081 15.545 1.00 0.00 WT1 H +ATOM 186 H2 TIP3W 928 2.117 2.999 14.422 1.00 0.00 WT1 H +ATOM 187 OH2 TIP3W 930 1.899 11.624 17.893 1.00 0.00 WT1 O +ATOM 188 H1 TIP3W 930 1.139 11.678 17.305 1.00 0.00 WT1 H +ATOM 189 H2 TIP3W 930 2.258 12.535 17.855 1.00 0.00 WT1 H +ATOM 190 OH2 TIP3W 932 9.220 13.904 17.340 1.00 0.00 WT1 O +ATOM 191 H1 TIP3W 932 10.062 14.198 17.738 1.00 0.00 WT1 H +ATOM 192 H2 TIP3W 932 9.394 12.999 17.102 1.00 0.00 WT1 H +ATOM 193 OH2 TIP3W 933 3.458 9.868 22.419 1.00 0.00 WT1 O +ATOM 194 H1 TIP3W 933 4.398 10.016 22.654 1.00 0.00 WT1 H +ATOM 195 H2 TIP3W 933 3.448 10.189 21.495 1.00 0.00 WT1 H +ATOM 196 OH2 TIP3W 947 15.430 3.274 7.407 1.00 0.00 WT1 O +ATOM 197 H1 TIP3W 947 15.458 2.741 8.157 1.00 0.00 WT1 H +ATOM 198 H2 TIP3W 947 15.933 2.740 6.770 1.00 0.00 WT1 H +ATOM 199 OH2 TIP3W 948 13.134 4.535 6.559 1.00 0.00 WT1 O +ATOM 200 H1 TIP3W 948 12.434 3.932 6.938 1.00 0.00 WT1 H +ATOM 201 H2 TIP3W 948 13.959 4.162 6.965 1.00 0.00 WT1 H +ATOM 202 OH2 TIP3W 951 10.295 14.066 14.320 1.00 0.00 WT1 O +ATOM 203 H1 TIP3W 951 10.592 14.067 15.226 1.00 0.00 WT1 H +ATOM 204 H2 TIP3W 951 9.322 14.226 14.350 1.00 0.00 WT1 H +ATOM 205 OH2 TIP3W 964 7.830 19.751 1.995 1.00 0.00 WT1 O +ATOM 206 H1 TIP3W 964 7.257 19.870 1.247 1.00 0.00 WT1 H +ATOM 207 H2 TIP3W 964 8.329 18.923 1.885 1.00 0.00 WT1 H +ATOM 208 OH2 TIP3W 972 15.027 11.249 9.806 1.00 0.00 WT1 O +ATOM 209 H1 TIP3W 972 15.636 10.953 9.104 1.00 0.00 WT1 H +ATOM 210 H2 TIP3W 972 14.929 12.194 9.545 1.00 0.00 WT1 H +ATOM 211 OH2 TIP3W 974 10.274 11.448 20.959 1.00 0.00 WT1 O +ATOM 212 H1 TIP3W 974 10.893 11.073 21.654 1.00 0.00 WT1 H +ATOM 213 H2 TIP3W 974 10.344 10.891 20.238 1.00 0.00 WT1 H +ATOM 214 OH2 TIP3W 975 11.473 6.075 21.702 1.00 0.00 WT1 O +ATOM 215 H1 TIP3W 975 12.046 5.667 22.431 1.00 0.00 WT1 H +ATOM 216 H2 TIP3W 975 10.554 5.939 22.100 1.00 0.00 WT1 H +ATOM 217 OH2 TIP3W 995 6.800 16.659 17.184 1.00 0.00 WT1 O +ATOM 218 H1 TIP3W 995 7.143 16.649 16.327 1.00 0.00 WT1 H +ATOM 219 H2 TIP3W 995 7.109 17.502 17.568 1.00 0.00 WT1 H +ATOM 220 OH2 TIP3W1007 14.603 18.110 3.213 1.00 0.00 WT1 O +ATOM 221 H1 TIP3W1007 14.275 17.655 3.963 1.00 0.00 WT1 H +ATOM 222 H2 TIP3W1007 13.842 18.606 2.878 1.00 0.00 WT1 H +ATOM 223 OH2 TIP3W1011 4.753 20.139 5.475 1.00 0.00 WT1 O +ATOM 224 H1 TIP3W1011 4.769 21.053 5.846 1.00 0.00 WT1 H +ATOM 225 H2 TIP3W1011 5.663 20.031 5.201 1.00 0.00 WT1 H +ATOM 226 OH2 TIP3W1013 1.615 17.355 14.355 1.00 0.00 WT1 O +ATOM 227 H1 TIP3W1013 1.225 16.480 14.420 1.00 0.00 WT1 H +ATOM 228 H2 TIP3W1013 0.859 17.984 14.051 1.00 0.00 WT1 H +ATOM 229 OH2 TIP3W1014 11.087 15.787 20.150 1.00 0.00 WT1 O +ATOM 230 H1 TIP3W1014 11.221 14.877 19.698 1.00 0.00 WT1 H +ATOM 231 H2 TIP3W1014 11.936 15.940 20.591 1.00 0.00 WT1 H +ATOM 232 OH2 TIP3W1017 9.784 18.060 16.439 1.00 0.00 WT1 O +ATOM 233 H1 TIP3W1017 10.576 18.166 15.922 1.00 0.00 WT1 H +ATOM 234 H2 TIP3W1017 9.941 18.584 17.234 1.00 0.00 WT1 H +ATOM 235 OH2 TIP3W1018 2.369 19.620 10.838 1.00 0.00 WT1 O +ATOM 236 H1 TIP3W1018 2.051 19.425 11.701 1.00 0.00 WT1 H +ATOM 237 H2 TIP3W1018 3.347 19.717 10.923 1.00 0.00 WT1 H +ATOM 238 OH2 TIP3W1027 15.158 15.218 1.453 1.00 0.00 WT1 O +ATOM 239 H1 TIP3W1027 15.286 16.123 1.160 1.00 0.00 WT1 H +ATOM 240 H2 TIP3W1027 14.175 15.219 1.587 1.00 0.00 WT1 H +ATOM 241 OH2 TIP3W1032 7.929 9.601 4.322 1.00 0.00 WT1 O +ATOM 242 H1 TIP3W1032 7.364 10.340 3.912 1.00 0.00 WT1 H +ATOM 243 H2 TIP3W1032 7.318 9.011 4.820 1.00 0.00 WT1 H +ATOM 244 OH2 TIP3W1053 11.585 23.121 19.455 1.00 0.00 WT1 O +ATOM 245 H1 TIP3W1053 12.413 23.205 19.982 1.00 0.00 WT1 H +ATOM 246 H2 TIP3W1053 10.816 23.266 20.095 1.00 0.00 WT1 H +ATOM 247 OH2 TIP3W1301 3.320 1.439 3.693 1.00 0.00 WT1 O +ATOM 248 H1 TIP3W1301 3.018 1.263 2.795 1.00 0.00 WT1 H +ATOM 249 H2 TIP3W1301 4.218 1.737 3.533 1.00 0.00 WT1 H +ATOM 250 OH2 TIP3W1308 8.378 22.836 14.074 1.00 0.00 WT1 O +ATOM 251 H1 TIP3W1308 9.127 23.085 13.478 1.00 0.00 WT1 H +ATOM 252 H2 TIP3W1308 7.806 23.652 14.112 1.00 0.00 WT1 H +ATOM 253 OH2 TIP3W1328 4.539 2.605 8.295 1.00 0.00 WT1 O +ATOM 254 H1 TIP3W1328 5.460 2.702 8.123 1.00 0.00 WT1 H +ATOM 255 H2 TIP3W1328 4.434 1.616 8.363 1.00 0.00 WT1 H +ATOM 256 OH2 TIP3W1344 8.883 21.581 5.760 1.00 0.00 WT1 O +ATOM 257 H1 TIP3W1344 8.705 22.232 6.446 1.00 0.00 WT1 H +ATOM 258 H2 TIP3W1344 9.357 22.008 5.077 1.00 0.00 WT1 H +ATOM 259 OH2 TIP3W1349 12.793 13.364 12.168 1.00 0.00 WT1 O +ATOM 260 H1 TIP3W1349 12.787 13.548 11.223 1.00 0.00 WT1 H +ATOM 261 H2 TIP3W1349 11.995 13.794 12.399 1.00 0.00 WT1 H +ATOM 262 OH2 TIP3W1352 6.667 7.547 9.646 1.00 0.00 WT1 O +ATOM 263 H1 TIP3W1352 6.103 6.975 10.296 1.00 0.00 WT1 H +ATOM 264 H2 TIP3W1352 7.558 7.292 10.046 1.00 0.00 WT1 H +ATOM 265 OH2 TIP3W1354 0.182 23.403 21.361 1.00 0.00 WT1 O +ATOM 266 H1 TIP3W1354 0.301 23.585 22.346 1.00 0.00 WT1 H +ATOM 267 H2 TIP3W1354 1.001 22.867 21.220 1.00 0.00 WT1 H +ATOM 268 OH2 TIP3W1355 11.347 16.007 23.148 1.00 0.00 WT1 O +ATOM 269 H1 TIP3W1355 11.779 15.126 23.087 1.00 0.00 WT1 H +ATOM 270 H2 TIP3W1355 10.586 15.923 22.581 1.00 0.00 WT1 H +ATOM 271 OH2 TIP3W1367 10.129 17.485 6.550 1.00 0.00 WT1 O +ATOM 272 H1 TIP3W1367 9.231 17.467 6.920 1.00 0.00 WT1 H +ATOM 273 H2 TIP3W1367 10.108 16.702 5.985 1.00 0.00 WT1 H +ATOM 274 OH2 TIP3W1370 4.654 5.717 5.023 1.00 0.00 WT1 O +ATOM 275 H1 TIP3W1370 5.059 5.126 4.395 1.00 0.00 WT1 H +ATOM 276 H2 TIP3W1370 5.409 5.785 5.634 1.00 0.00 WT1 H +ATOM 277 OH2 TIP3W1371 12.336 14.905 9.350 1.00 0.00 WT1 O +ATOM 278 H1 TIP3W1371 11.849 15.588 8.883 1.00 0.00 WT1 H +ATOM 279 H2 TIP3W1371 11.568 14.375 9.770 1.00 0.00 WT1 H +ATOM 280 OH2 TIP3W1374 5.488 14.255 13.212 1.00 0.00 WT1 O +ATOM 281 H1 TIP3W1374 6.279 14.126 13.709 1.00 0.00 WT1 H +ATOM 282 H2 TIP3W1374 4.864 13.991 13.878 1.00 0.00 WT1 H +ATOM 283 OH2 TIP3W1387 3.686 8.353 3.401 1.00 0.00 WT1 O +ATOM 284 H1 TIP3W1387 4.494 7.930 3.084 1.00 0.00 WT1 H +ATOM 285 H2 TIP3W1387 3.041 7.727 3.197 1.00 0.00 WT1 H +ATOM 286 OH2 TIP3W1388 15.005 14.526 19.133 1.00 0.00 WT1 O +ATOM 287 H1 TIP3W1388 15.742 13.941 19.238 1.00 0.00 WT1 H +ATOM 288 H2 TIP3W1388 14.746 14.453 18.188 1.00 0.00 WT1 H +ATOM 289 OH2 TIP3W1389 15.427 13.899 13.418 1.00 0.00 WT1 O +ATOM 290 H1 TIP3W1389 15.598 14.703 13.915 1.00 0.00 WT1 H +ATOM 291 H2 TIP3W1389 14.569 14.032 12.994 1.00 0.00 WT1 H +ATOM 292 OH2 TIP3W1392 15.117 16.342 15.320 1.00 0.00 WT1 O +ATOM 293 H1 TIP3W1392 14.190 16.658 15.235 1.00 0.00 WT1 H +ATOM 294 H2 TIP3W1392 15.725 17.080 14.950 1.00 0.00 WT1 H +ATOM 295 OH2 TIP3W1407 13.263 23.513 7.326 1.00 0.00 WT1 O +ATOM 296 H1 TIP3W1407 14.083 23.900 7.689 1.00 0.00 WT1 H +ATOM 297 H2 TIP3W1407 13.669 22.803 6.739 1.00 0.00 WT1 H +ATOM 298 OH2 TIP3W1411 10.030 11.441 3.434 1.00 0.00 WT1 O +ATOM 299 H1 TIP3W1411 9.274 10.827 3.422 1.00 0.00 WT1 H +ATOM 300 H2 TIP3W1411 10.533 11.362 2.661 1.00 0.00 WT1 H +ATOM 301 OH2 TIP3W1412 10.550 9.544 11.315 1.00 0.00 WT1 O +ATOM 302 H1 TIP3W1412 10.055 10.343 11.396 1.00 0.00 WT1 H +ATOM 303 H2 TIP3W1412 11.460 9.846 11.337 1.00 0.00 WT1 H +ATOM 304 OH2 TIP3W1414 2.005 17.796 21.122 1.00 0.00 WT1 O +ATOM 305 H1 TIP3W1414 2.773 17.325 21.598 1.00 0.00 WT1 H +ATOM 306 H2 TIP3W1414 2.173 18.758 21.265 1.00 0.00 WT1 H +ATOM 307 OH2 TIP3W1415 13.553 15.240 21.435 1.00 0.00 WT1 O +ATOM 308 H1 TIP3W1415 14.103 14.959 20.726 1.00 0.00 WT1 H +ATOM 309 H2 TIP3W1415 13.422 14.470 21.979 1.00 0.00 WT1 H +ATOM 310 OH2 TIP3W1418 11.456 2.350 19.585 1.00 0.00 WT1 O +ATOM 311 H1 TIP3W1418 10.731 2.931 19.730 1.00 0.00 WT1 H +ATOM 312 H2 TIP3W1418 11.546 1.862 20.401 1.00 0.00 WT1 H +ATOM 313 OH2 TIP3W1428 13.068 2.914 10.149 1.00 0.00 WT1 O +ATOM 314 H1 TIP3W1428 12.803 2.473 9.295 1.00 0.00 WT1 H +ATOM 315 H2 TIP3W1428 14.010 2.849 10.112 1.00 0.00 WT1 H +ATOM 316 OH2 TIP3W1429 5.450 9.067 5.337 1.00 0.00 WT1 O +ATOM 317 H1 TIP3W1429 4.722 8.840 4.711 1.00 0.00 WT1 H +ATOM 318 H2 TIP3W1429 4.939 8.770 6.117 1.00 0.00 WT1 H +ATOM 319 OH2 TIP3W1433 3.297 18.771 17.303 1.00 0.00 WT1 O +ATOM 320 H1 TIP3W1433 3.913 19.272 17.825 1.00 0.00 WT1 H +ATOM 321 H2 TIP3W1433 3.616 18.935 16.408 1.00 0.00 WT1 H +ATOM 322 OH2 TIP3W1435 6.597 15.954 21.463 1.00 0.00 WT1 O +ATOM 323 H1 TIP3W1435 7.157 15.160 21.200 1.00 0.00 WT1 H +ATOM 324 H2 TIP3W1435 7.205 16.451 22.021 1.00 0.00 WT1 H +ATOM 325 OH2 TIP3W1440 1.443 3.980 18.627 1.00 0.00 WT1 O +ATOM 326 H1 TIP3W1440 1.536 3.050 18.247 1.00 0.00 WT1 H +ATOM 327 H2 TIP3W1440 0.589 4.282 18.256 1.00 0.00 WT1 H +ATOM 328 OH2 TIP3W1451 3.248 22.876 3.701 1.00 0.00 WT1 O +ATOM 329 H1 TIP3W1451 2.662 22.334 4.248 1.00 0.00 WT1 H +ATOM 330 H2 TIP3W1451 4.106 22.410 3.781 1.00 0.00 WT1 H +ATOM 331 OH2 TIP3W1454 8.943 19.607 9.393 1.00 0.00 WT1 O +ATOM 332 H1 TIP3W1454 9.890 19.666 9.174 1.00 0.00 WT1 H +ATOM 333 H2 TIP3W1454 8.551 19.202 8.586 1.00 0.00 WT1 H +ATOM 334 OH2 TIP3W1455 7.534 23.313 22.010 1.00 0.00 WT1 O +ATOM 335 H1 TIP3W1455 7.309 22.777 22.738 1.00 0.00 WT1 H +ATOM 336 H2 TIP3W1455 6.697 23.403 21.532 1.00 0.00 WT1 H +ATOM 337 OH2 TIP3W1457 13.340 13.560 16.477 1.00 0.00 WT1 O +ATOM 338 H1 TIP3W1457 13.400 13.568 15.542 1.00 0.00 WT1 H +ATOM 339 H2 TIP3W1457 12.852 14.406 16.633 1.00 0.00 WT1 H +ATOM 340 OH2 TIP3W1458 8.344 7.845 20.429 1.00 0.00 WT1 O +ATOM 341 H1 TIP3W1458 8.479 8.292 21.236 1.00 0.00 WT1 H +ATOM 342 H2 TIP3W1458 9.102 8.059 19.900 1.00 0.00 WT1 H +ATOM 343 OH2 TIP3W1474 6.901 21.557 9.326 1.00 0.00 WT1 O +ATOM 344 H1 TIP3W1474 7.410 20.744 9.384 1.00 0.00 WT1 H +ATOM 345 H2 TIP3W1474 7.474 22.077 8.759 1.00 0.00 WT1 H +ATOM 346 OH2 TIP3W1494 14.403 7.815 15.212 1.00 0.00 WT1 O +ATOM 347 H1 TIP3W1494 13.532 8.206 14.911 1.00 0.00 WT1 H +ATOM 348 H2 TIP3W1494 14.885 7.681 14.373 1.00 0.00 WT1 H +ATOM 349 OH2 TIP3W1497 6.857 11.138 6.829 1.00 0.00 WT1 O +ATOM 350 H1 TIP3W1497 6.107 11.750 6.800 1.00 0.00 WT1 H +ATOM 351 H2 TIP3W1497 6.480 10.387 6.353 1.00 0.00 WT1 H +ATOM 352 OH2 TIP3W1512 10.309 21.500 11.481 1.00 0.00 WT1 O +ATOM 353 H1 TIP3W1512 11.014 20.928 11.185 1.00 0.00 WT1 H +ATOM 354 H2 TIP3W1512 9.595 20.961 11.183 1.00 0.00 WT1 H +ATOM 355 OH2 TIP3W1532 13.235 22.943 15.633 1.00 0.00 WT1 O +ATOM 356 H1 TIP3W1532 12.613 22.525 16.194 1.00 0.00 WT1 H +ATOM 357 H2 TIP3W1532 14.027 22.981 16.180 1.00 0.00 WT1 H +ATOM 358 OH2 TIP3W1559 6.818 20.066 20.150 1.00 0.00 WT1 O +ATOM 359 H1 TIP3W1559 7.686 20.067 20.626 1.00 0.00 WT1 H +ATOM 360 H2 TIP3W1559 6.969 19.869 19.212 1.00 0.00 WT1 H +ATOM 361 OH2 TIP3W1611 7.975 20.030 22.745 1.00 0.00 WT1 O +ATOM 362 H1 TIP3W1611 8.632 20.654 22.435 1.00 0.00 WT1 H +ATOM 363 H2 TIP3W1611 7.441 20.490 23.501 1.00 0.00 WT1 H +ATOM 364 OH2 TIP3W1707 12.113 0.921 4.942 1.00 0.00 WT1 O +ATOM 365 H1 TIP3W1707 12.819 0.635 5.562 1.00 0.00 WT1 H +ATOM 366 H2 TIP3W1707 11.814 1.896 5.223 1.00 0.00 WT1 H +ATOM 367 OH2 TIP3W1723 9.197 4.375 15.964 1.00 0.00 WT1 O +ATOM 368 H1 TIP3W1723 9.163 3.590 15.387 1.00 0.00 WT1 H +ATOM 369 H2 TIP3W1723 8.516 4.167 16.604 1.00 0.00 WT1 H +ATOM 370 OH2 TIP3W1725 2.421 3.775 5.058 1.00 0.00 WT1 O +ATOM 371 H1 TIP3W1725 2.684 2.934 4.652 1.00 0.00 WT1 H +ATOM 372 H2 TIP3W1725 3.219 4.340 5.048 1.00 0.00 WT1 H +ATOM 373 OH2 TIP3W1729 6.794 6.875 22.997 1.00 0.00 WT1 O +ATOM 374 H1 TIP3W1729 7.166 7.815 23.093 1.00 0.00 WT1 H +ATOM 375 H2 TIP3W1729 5.834 7.029 23.036 1.00 0.00 WT1 H +ATOM 376 OH2 TIP3W1730 11.518 2.141 14.835 1.00 0.00 WT1 O +ATOM 377 H1 TIP3W1730 11.356 2.769 14.101 1.00 0.00 WT1 H +ATOM 378 H2 TIP3W1730 12.345 1.727 14.583 1.00 0.00 WT1 H +ATOM 379 OH2 TIP3W1733 3.174 1.584 16.976 1.00 0.00 WT1 O +ATOM 380 H1 TIP3W1733 2.370 2.077 16.810 1.00 0.00 WT1 H +ATOM 381 H2 TIP3W1733 3.270 0.961 16.252 1.00 0.00 WT1 H +ATOM 382 OH2 TIP3W1746 10.848 10.071 18.631 1.00 0.00 WT1 O +ATOM 383 H1 TIP3W1746 10.345 10.477 17.907 1.00 0.00 WT1 H +ATOM 384 H2 TIP3W1746 11.663 10.551 18.638 1.00 0.00 WT1 H +ATOM 385 OH2 TIP3W1752 12.069 8.766 23.082 1.00 0.00 WT1 O +ATOM 386 H1 TIP3W1752 12.023 9.290 23.888 1.00 0.00 WT1 H +ATOM 387 H2 TIP3W1752 11.590 7.956 23.400 1.00 0.00 WT1 H +ATOM 388 OH2 TIP3W1764 5.141 1.611 0.499 1.00 0.00 WT1 O +ATOM 389 H1 TIP3W1764 4.697 1.110 1.234 1.00 0.00 WT1 H +ATOM 390 H2 TIP3W1764 6.031 1.302 0.586 1.00 0.00 WT1 H +ATOM 391 OH2 TIP3W1771 2.509 3.505 12.910 1.00 0.00 WT1 O +ATOM 392 H1 TIP3W1771 2.114 4.138 12.315 1.00 0.00 WT1 H +ATOM 393 H2 TIP3W1771 2.715 2.712 12.383 1.00 0.00 WT1 H +ATOM 394 OH2 TIP3W1773 14.354 1.352 14.004 1.00 0.00 WT1 O +ATOM 395 H1 TIP3W1773 14.694 0.623 14.565 1.00 0.00 WT1 H +ATOM 396 H2 TIP3W1773 14.573 2.195 14.426 1.00 0.00 WT1 H +ATOM 397 OH2 TIP3W1788 14.578 23.489 17.850 1.00 0.00 WT1 O +ATOM 398 H1 TIP3W1788 15.476 23.267 17.861 1.00 0.00 WT1 H +ATOM 399 H2 TIP3W1788 14.359 23.484 18.771 1.00 0.00 WT1 H +ATOM 400 OH2 TIP3W1789 5.461 6.754 1.943 1.00 0.00 WT1 O +ATOM 401 H1 TIP3W1789 6.412 6.627 2.018 1.00 0.00 WT1 H +ATOM 402 H2 TIP3W1789 5.209 5.956 1.434 1.00 0.00 WT1 H +ATOM 403 OH2 TIP3W1795 14.101 1.902 22.316 1.00 0.00 WT1 O +ATOM 404 H1 TIP3W1795 14.886 2.398 22.002 1.00 0.00 WT1 H +ATOM 405 H2 TIP3W1795 14.108 1.041 21.813 1.00 0.00 WT1 H +ATOM 406 OH2 TIP3W1813 6.142 11.858 16.052 1.00 0.00 WT1 O +ATOM 407 H1 TIP3W1813 5.762 12.642 15.675 1.00 0.00 WT1 H +ATOM 408 H2 TIP3W1813 5.566 11.146 15.661 1.00 0.00 WT1 H +ATOM 409 OH2 TIP3W1814 11.187 19.104 18.681 1.00 0.00 WT1 O +ATOM 410 H1 TIP3W1814 12.029 18.566 18.863 1.00 0.00 WT1 H +ATOM 411 H2 TIP3W1814 10.574 18.773 19.364 1.00 0.00 WT1 H +ATOM 412 OH2 TIP3W1829 11.780 13.509 0.983 1.00 0.00 WT1 O +ATOM 413 H1 TIP3W1829 12.311 13.422 1.794 1.00 0.00 WT1 H +ATOM 414 H2 TIP3W1829 12.379 13.816 0.300 1.00 0.00 WT1 H +ATOM 415 OH2 TIP3W1830 13.410 13.796 3.206 1.00 0.00 WT1 O +ATOM 416 H1 TIP3W1830 12.860 13.342 3.952 1.00 0.00 WT1 H +ATOM 417 H2 TIP3W1830 14.378 13.624 3.486 1.00 0.00 WT1 H +ATOM 418 OH2 TIP3W1831 7.314 0.228 9.152 1.00 0.00 WT1 O +ATOM 419 H1 TIP3W1831 7.447 0.196 8.157 1.00 0.00 WT1 H +ATOM 420 H2 TIP3W1831 8.219 0.336 9.426 1.00 0.00 WT1 H +ATOM 421 OH2 TIP3W1853 0.289 10.538 13.468 1.00 0.00 WT1 O +ATOM 422 H1 TIP3W1853 0.286 10.937 12.602 1.00 0.00 WT1 H +ATOM 423 H2 TIP3W1853 1.262 10.357 13.669 1.00 0.00 WT1 H +ATOM 424 OH2 TIP3W1856 12.440 12.407 5.370 1.00 0.00 WT1 O +ATOM 425 H1 TIP3W1856 11.652 11.887 5.105 1.00 0.00 WT1 H +ATOM 426 H2 TIP3W1856 12.893 11.867 5.977 1.00 0.00 WT1 H +ATOM 427 OH2 TIP3W1871 6.968 11.629 2.353 1.00 0.00 WT1 O +ATOM 428 H1 TIP3W1871 6.575 10.896 1.807 1.00 0.00 WT1 H +ATOM 429 H2 TIP3W1871 7.083 12.290 1.590 1.00 0.00 WT1 H +ATOM 430 OH2 TIP3W1873 13.533 10.550 7.160 1.00 0.00 WT1 O +ATOM 431 H1 TIP3W1873 12.608 10.309 7.490 1.00 0.00 WT1 H +ATOM 432 H2 TIP3W1873 14.008 10.940 7.925 1.00 0.00 WT1 H +ATOM 433 OH2 TIP3W1874 13.043 18.831 22.933 1.00 0.00 WT1 O +ATOM 434 H1 TIP3W1874 13.439 17.936 22.986 1.00 0.00 WT1 H +ATOM 435 H2 TIP3W1874 12.139 18.764 23.145 1.00 0.00 WT1 H +ATOM 436 OH2 TIP3W1894 11.706 15.811 16.829 1.00 0.00 WT1 O +ATOM 437 H1 TIP3W1894 10.892 16.347 16.590 1.00 0.00 WT1 H +ATOM 438 H2 TIP3W1894 12.344 16.466 17.162 1.00 0.00 WT1 H +ATOM 439 OH2 TIP3W1911 11.642 19.030 4.866 1.00 0.00 WT1 O +ATOM 440 H1 TIP3W1911 10.752 18.786 5.209 1.00 0.00 WT1 H +ATOM 441 H2 TIP3W1911 11.534 19.147 3.897 1.00 0.00 WT1 H +ATOM 442 OH2 TIP3W1912 13.550 21.522 9.565 1.00 0.00 WT1 O +ATOM 443 H1 TIP3W1912 13.279 21.744 8.655 1.00 0.00 WT1 H +ATOM 444 H2 TIP3W1912 13.859 22.419 9.914 1.00 0.00 WT1 H +ATOM 445 OH2 TIP3W1914 12.001 20.877 14.108 1.00 0.00 WT1 O +ATOM 446 H1 TIP3W1914 12.060 21.566 14.774 1.00 0.00 WT1 H +ATOM 447 H2 TIP3W1914 11.186 21.104 13.629 1.00 0.00 WT1 H +ATOM 448 OH2 TIP3W1915 12.814 17.906 7.383 1.00 0.00 WT1 O +ATOM 449 H1 TIP3W1915 13.379 17.410 6.688 1.00 0.00 WT1 H +ATOM 450 H2 TIP3W1915 11.963 17.994 6.954 1.00 0.00 WT1 H +ATOM 451 OH2 TIP3W1952 15.989 19.751 4.862 1.00 0.00 WT1 O +ATOM 452 H1 TIP3W1952 15.952 20.632 4.460 1.00 0.00 WT1 H +ATOM 453 H2 TIP3W1952 15.557 19.210 4.188 1.00 0.00 WT1 H +ATOM 454 OH2 TIP3W2123 10.963 1.737 11.790 1.00 0.00 WT1 O +ATOM 455 H1 TIP3W2123 10.319 2.240 11.334 1.00 0.00 WT1 H +ATOM 456 H2 TIP3W2123 11.709 2.167 11.210 1.00 0.00 WT1 H +ATOM 457 OH2 TIP3W2163 5.526 8.369 14.858 1.00 0.00 WT1 O +ATOM 458 H1 TIP3W2163 4.950 8.218 14.072 1.00 0.00 WT1 H +ATOM 459 H2 TIP3W2163 4.945 8.919 15.363 1.00 0.00 WT1 H +ATOM 460 OH2 TIP3W2165 14.776 4.939 12.443 1.00 0.00 WT1 O +ATOM 461 H1 TIP3W2165 14.636 5.952 12.252 1.00 0.00 WT1 H +ATOM 462 H2 TIP3W2165 13.865 4.712 12.604 1.00 0.00 WT1 H +ATOM 463 OH2 TIP3W2167 7.529 4.508 1.396 1.00 0.00 WT1 O +ATOM 464 H1 TIP3W2167 8.313 4.582 0.857 1.00 0.00 WT1 H +ATOM 465 H2 TIP3W2167 6.783 4.511 0.768 1.00 0.00 WT1 H +ATOM 466 OH2 TIP3W2172 11.435 0.836 22.059 1.00 0.00 WT1 O +ATOM 467 H1 TIP3W2172 11.858 0.103 21.657 1.00 0.00 WT1 H +ATOM 468 H2 TIP3W2172 12.219 1.281 22.508 1.00 0.00 WT1 H +ATOM 469 OH2 TIP3W2227 11.200 4.151 3.471 1.00 0.00 WT1 O +ATOM 470 H1 TIP3W2227 12.053 4.360 3.928 1.00 0.00 WT1 H +ATOM 471 H2 TIP3W2227 10.572 4.426 4.138 1.00 0.00 WT1 H +ATOM 472 OH2 TIP3W2231 4.884 4.081 13.713 1.00 0.00 WT1 O +ATOM 473 H1 TIP3W2231 4.970 4.746 14.373 1.00 0.00 WT1 H +ATOM 474 H2 TIP3W2231 3.932 3.975 13.593 1.00 0.00 WT1 H +ATOM 475 OH2 TIP3W2244 13.867 4.624 3.954 1.00 0.00 WT1 O +ATOM 476 H1 TIP3W2244 14.067 4.641 4.904 1.00 0.00 WT1 H +ATOM 477 H2 TIP3W2244 14.122 5.494 3.648 1.00 0.00 WT1 H +ATOM 478 OH2 TIP3W2270 3.174 11.159 5.954 1.00 0.00 WT1 O +ATOM 479 H1 TIP3W2270 3.904 11.073 5.352 1.00 0.00 WT1 H +ATOM 480 H2 TIP3W2270 3.204 12.104 6.129 1.00 0.00 WT1 H +ATOM 481 OH2 TIP3W2272 12.922 2.911 17.412 1.00 0.00 WT1 O +ATOM 482 H1 TIP3W2272 12.421 2.431 18.089 1.00 0.00 WT1 H +ATOM 483 H2 TIP3W2272 12.240 2.996 16.701 1.00 0.00 WT1 H +ATOM 484 OH2 TIP3W2277 13.644 7.961 20.946 1.00 0.00 WT1 O +ATOM 485 H1 TIP3W2277 13.183 7.158 20.680 1.00 0.00 WT1 H +ATOM 486 H2 TIP3W2277 13.018 8.315 21.687 1.00 0.00 WT1 H +ATOM 487 OH2 TIP3W2280 6.612 3.396 17.042 1.00 0.00 WT1 O +ATOM 488 H1 TIP3W2280 6.138 2.987 17.830 1.00 0.00 WT1 H +ATOM 489 H2 TIP3W2280 6.248 2.883 16.306 1.00 0.00 WT1 H +ATOM 490 OH2 TIP3W2288 3.628 15.453 9.684 1.00 0.00 WT1 O +ATOM 491 H1 TIP3W2288 3.604 16.368 9.365 1.00 0.00 WT1 H +ATOM 492 H2 TIP3W2288 3.266 15.478 10.592 1.00 0.00 WT1 H +ATOM 493 OH2 TIP3W2293 1.641 18.264 8.136 1.00 0.00 WT1 O +ATOM 494 H1 TIP3W2293 0.755 18.490 8.008 1.00 0.00 WT1 H +ATOM 495 H2 TIP3W2293 1.981 19.003 8.665 1.00 0.00 WT1 H +ATOM 496 OH2 TIP3W2295 8.716 0.819 21.571 1.00 0.00 WT1 O +ATOM 497 H1 TIP3W2295 8.359 0.399 22.460 1.00 0.00 WT1 H +ATOM 498 H2 TIP3W2295 9.622 1.046 21.690 1.00 0.00 WT1 H +ATOM 499 OH2 TIP3W2309 14.269 10.001 4.369 1.00 0.00 WT1 O +ATOM 500 H1 TIP3W2309 14.973 10.528 4.752 1.00 0.00 WT1 H +ATOM 501 H2 TIP3W2309 13.690 9.859 5.092 1.00 0.00 WT1 H +ATOM 502 OH2 TIP3W2311 14.691 13.817 9.050 1.00 0.00 WT1 O +ATOM 503 H1 TIP3W2311 15.162 14.372 8.385 1.00 0.00 WT1 H +ATOM 504 H2 TIP3W2311 13.821 14.250 9.113 1.00 0.00 WT1 H +ATOM 505 OH2 TIP3W2316 12.273 5.424 10.404 1.00 0.00 WT1 O +ATOM 506 H1 TIP3W2316 12.384 4.472 10.210 1.00 0.00 WT1 H +ATOM 507 H2 TIP3W2316 13.153 5.714 10.501 1.00 0.00 WT1 H +ATOM 508 OH2 TIP3W2317 3.759 13.253 15.143 1.00 0.00 WT1 O +ATOM 509 H1 TIP3W2317 3.552 13.546 16.059 1.00 0.00 WT1 H +ATOM 510 H2 TIP3W2317 2.862 13.321 14.740 1.00 0.00 WT1 H +ATOM 511 OH2 TIP3W2335 7.319 14.432 15.015 1.00 0.00 WT1 O +ATOM 512 H1 TIP3W2335 7.633 15.319 14.742 1.00 0.00 WT1 H +ATOM 513 H2 TIP3W2335 7.702 14.303 15.933 1.00 0.00 WT1 H +ATOM 514 OH2 TIP3W2357 3.117 11.819 10.070 1.00 0.00 WT1 O +ATOM 515 H1 TIP3W2357 3.490 12.496 9.523 1.00 0.00 WT1 H +ATOM 516 H2 TIP3W2357 3.937 11.583 10.539 1.00 0.00 WT1 H +ATOM 517 OH2 TIP3W2358 0.549 16.393 10.366 1.00 0.00 WT1 O +ATOM 518 H1 TIP3W2358 1.292 16.322 11.016 1.00 0.00 WT1 H +ATOM 519 H2 TIP3W2358 0.665 17.283 9.972 1.00 0.00 WT1 H +ATOM 520 OH2 TIP3W2607 10.050 5.605 5.758 1.00 0.00 WT1 O +ATOM 521 H1 TIP3W2607 10.155 6.554 5.556 1.00 0.00 WT1 H +ATOM 522 H2 TIP3W2607 10.797 5.389 6.309 1.00 0.00 WT1 H +ATOM 523 OH2 TIP3W2608 7.881 3.518 5.700 1.00 0.00 WT1 O +ATOM 524 H1 TIP3W2608 8.550 4.225 5.812 1.00 0.00 WT1 H +ATOM 525 H2 TIP3W2608 7.070 3.834 6.169 1.00 0.00 WT1 H +ATOM 526 OH2 TIP3W2634 8.559 3.515 11.535 1.00 0.00 WT1 O +ATOM 527 H1 TIP3W2634 8.435 4.298 12.155 1.00 0.00 WT1 H +ATOM 528 H2 TIP3W2634 7.955 2.899 11.952 1.00 0.00 WT1 H +ATOM 529 OH2 TIP3W2669 13.039 10.511 11.777 1.00 0.00 WT1 O +ATOM 530 H1 TIP3W2669 13.825 10.589 11.282 1.00 0.00 WT1 H +ATOM 531 H2 TIP3W2669 12.883 11.473 11.916 1.00 0.00 WT1 H +ATOM 532 OH2 TIP3W2691 15.316 3.976 15.033 1.00 0.00 WT1 O +ATOM 533 H1 TIP3W2691 15.353 4.265 14.065 1.00 0.00 WT1 H +ATOM 534 H2 TIP3W2691 14.585 4.533 15.460 1.00 0.00 WT1 H +ATOM 535 OH2 TIP3W2694 8.400 5.552 13.557 1.00 0.00 WT1 O +ATOM 536 H1 TIP3W2694 9.070 5.240 14.185 1.00 0.00 WT1 H +ATOM 537 H2 TIP3W2694 7.739 5.945 14.163 1.00 0.00 WT1 H +ATOM 538 OH2 TIP3W2714 4.281 21.161 19.066 1.00 0.00 WT1 O +ATOM 539 H1 TIP3W2714 5.157 21.058 19.381 1.00 0.00 WT1 H +ATOM 540 H2 TIP3W2714 4.169 22.110 18.904 1.00 0.00 WT1 H +ATOM 541 OH2 TIP3W2732 13.870 7.474 12.187 1.00 0.00 WT1 O +ATOM 542 H1 TIP3W2732 13.209 8.073 12.633 1.00 0.00 WT1 H +ATOM 543 H2 TIP3W2732 14.457 8.029 11.659 1.00 0.00 WT1 H +ATOM 544 OH2 TIP3W2735 13.600 17.247 9.998 1.00 0.00 WT1 O +ATOM 545 H1 TIP3W2735 13.256 16.385 10.107 1.00 0.00 WT1 H +ATOM 546 H2 TIP3W2735 13.616 17.337 9.047 1.00 0.00 WT1 H +ATOM 547 OH2 TIP3W2758 10.099 18.083 21.099 1.00 0.00 WT1 O +ATOM 548 H1 TIP3W2758 10.453 17.258 20.699 1.00 0.00 WT1 H +ATOM 549 H2 TIP3W2758 9.398 17.746 21.690 1.00 0.00 WT1 H +ATOM 550 OH2 TIP3W2778 15.465 7.955 17.814 1.00 0.00 WT1 O +ATOM 551 H1 TIP3W2778 15.150 7.979 16.932 1.00 0.00 WT1 H +ATOM 552 H2 TIP3W2778 14.706 7.563 18.306 1.00 0.00 WT1 H +ATOM 553 OH2 TIP3W3010 9.016 4.086 8.814 1.00 0.00 WT1 O +ATOM 554 H1 TIP3W3010 9.377 5.001 8.813 1.00 0.00 WT1 H +ATOM 555 H2 TIP3W3010 8.726 3.741 9.661 1.00 0.00 WT1 H +ATOM 556 OH2 TIP3W3072 6.439 5.144 7.455 1.00 0.00 WT1 O +ATOM 557 H1 TIP3W3072 7.310 4.836 7.837 1.00 0.00 WT1 H +ATOM 558 H2 TIP3W3072 6.121 5.819 8.116 1.00 0.00 WT1 H +ATOM 559 OH2 TIP3W3096 13.331 4.563 23.416 1.00 0.00 WT1 O +ATOM 560 H1 TIP3W3096 14.315 4.772 23.360 1.00 0.00 WT1 H +ATOM 561 H2 TIP3W3096 13.215 3.678 23.134 1.00 0.00 WT1 H +ATOM 562 OH2 TIP3W3134 11.401 21.480 17.136 1.00 0.00 WT1 O +ATOM 563 H1 TIP3W3134 11.522 22.112 17.856 1.00 0.00 WT1 H +ATOM 564 H2 TIP3W3134 11.255 20.672 17.636 1.00 0.00 WT1 H +ATOM 565 OH2 TIP3W3173 12.076 4.645 13.566 1.00 0.00 WT1 O +ATOM 566 H1 TIP3W3173 12.000 5.522 13.148 1.00 0.00 WT1 H +ATOM 567 H2 TIP3W3173 11.827 4.835 14.443 1.00 0.00 WT1 H +ATOM 568 OH2 TIP3W3177 9.131 1.075 15.841 1.00 0.00 WT1 O +ATOM 569 H1 TIP3W3177 9.948 1.463 15.412 1.00 0.00 WT1 H +ATOM 570 H2 TIP3W3177 9.113 0.161 15.464 1.00 0.00 WT1 H +ATOM 571 OH2 TIP3W3196 7.694 8.338 16.687 1.00 0.00 WT1 O +ATOM 572 H1 TIP3W3196 7.323 8.081 17.508 1.00 0.00 WT1 H +ATOM 573 H2 TIP3W3196 6.991 8.476 16.072 1.00 0.00 WT1 H +ATOM 574 OH2 TIP3W3218 11.912 13.212 19.726 1.00 0.00 WT1 O +ATOM 575 H1 TIP3W3218 12.854 13.225 19.881 1.00 0.00 WT1 H +ATOM 576 H2 TIP3W3218 11.504 12.764 20.555 1.00 0.00 WT1 H +ATOM 577 OH2 TIP3W3223 5.115 19.820 22.632 1.00 0.00 WT1 O +ATOM 578 H1 TIP3W3223 4.270 19.752 22.092 1.00 0.00 WT1 H +ATOM 579 H2 TIP3W3223 5.800 19.585 21.996 1.00 0.00 WT1 H +ATOM 580 OH2 TIP3W3303 14.170 23.047 20.478 1.00 0.00 WT1 O +ATOM 581 H1 TIP3W3303 15.015 22.883 20.902 1.00 0.00 WT1 H +ATOM 582 H2 TIP3W3303 13.757 22.177 20.579 1.00 0.00 WT1 H +ATOM 583 OH2 TIP3W3304 13.163 20.489 20.636 1.00 0.00 WT1 O +ATOM 584 H1 TIP3W3304 12.450 20.171 20.104 1.00 0.00 WT1 H +ATOM 585 H2 TIP3W3304 13.220 19.875 21.393 1.00 0.00 WT1 H +ATOM 586 OH2 TIP3W3447 11.316 2.273 7.956 1.00 0.00 WT1 O +ATOM 587 H1 TIP3W3447 11.391 1.358 8.151 1.00 0.00 WT1 H +ATOM 588 H2 TIP3W3447 10.423 2.479 8.181 1.00 0.00 WT1 H +ATOM 589 OH2 TIP3W3545 10.407 6.649 8.888 1.00 0.00 WT1 O +ATOM 590 H1 TIP3W3545 9.810 7.215 9.386 1.00 0.00 WT1 H +ATOM 591 H2 TIP3W3545 11.077 6.417 9.547 1.00 0.00 WT1 H +ATOM 592 OH2 TIP3W3596 7.574 19.420 4.717 1.00 0.00 WT1 O +ATOM 593 H1 TIP3W3596 7.704 19.335 3.679 1.00 0.00 WT1 H +ATOM 594 H2 TIP3W3596 7.970 20.255 4.957 1.00 0.00 WT1 H +ATOM 595 OH2 TIP3W3650 12.254 19.676 2.229 1.00 0.00 WT1 O +ATOM 596 H1 TIP3W3650 12.678 20.538 2.358 1.00 0.00 WT1 H +ATOM 597 H2 TIP3W3650 12.115 19.535 1.250 1.00 0.00 WT1 H +ATOM 598 OH2 TIP3W3660 14.036 7.730 6.644 1.00 0.00 WT1 O +ATOM 599 H1 TIP3W3660 14.358 7.138 7.346 1.00 0.00 WT1 H +ATOM 600 H2 TIP3W3660 13.886 8.589 7.123 1.00 0.00 WT1 H +ATOM 601 OH2 TIP3W3977 8.900 7.310 11.290 1.00 0.00 WT1 O +ATOM 602 H1 TIP3W3977 8.739 6.706 12.078 1.00 0.00 WT1 H +ATOM 603 H2 TIP3W3977 9.555 8.003 11.531 1.00 0.00 WT1 H +ATOM 604 OH2 TIP3W4012 9.495 14.416 1.979 1.00 0.00 WT1 O +ATOM 605 H1 TIP3W4012 10.354 14.203 1.548 1.00 0.00 WT1 H +ATOM 606 H2 TIP3W4012 9.165 13.566 2.099 1.00 0.00 WT1 H +ATOM 607 OH2 TIP3W4036 13.605 5.353 19.280 1.00 0.00 WT1 O +ATOM 608 H1 TIP3W4036 13.658 4.527 18.812 1.00 0.00 WT1 H +ATOM 609 H2 TIP3W4036 12.688 5.367 19.516 1.00 0.00 WT1 H +ATOM 610 OH2 TIP3W4074 7.334 17.973 7.090 1.00 0.00 WT1 O +ATOM 611 H1 TIP3W4074 7.571 18.390 6.200 1.00 0.00 WT1 H +ATOM 612 H2 TIP3W4074 6.533 17.444 6.885 1.00 0.00 WT1 H +ATOM 613 OH2 TIP3W4077 13.912 11.040 17.383 1.00 0.00 WT1 O +ATOM 614 H1 TIP3W4077 13.913 10.932 16.423 1.00 0.00 WT1 H +ATOM 615 H2 TIP3W4077 13.612 11.935 17.518 1.00 0.00 WT1 H +ATOM 616 OH2 TIP3W4501 14.682 11.334 14.388 1.00 0.00 WT1 O +ATOM 617 H1 TIP3W4501 15.236 11.941 13.876 1.00 0.00 WT1 H +ATOM 618 H2 TIP3W4501 14.266 10.683 13.763 1.00 0.00 WT1 H +ATOM 619 OH2 TIP3W4515 12.414 9.004 13.909 1.00 0.00 WT1 O +ATOM 620 H1 TIP3W4515 11.523 8.931 14.184 1.00 0.00 WT1 H +ATOM 621 H2 TIP3W4515 12.375 9.766 13.286 1.00 0.00 WT1 H +ATOM 622 OH2 TIP3W4809 15.898 3.293 1.648 1.00 0.00 WT1 O +ATOM 623 H1 TIP3W4809 15.837 3.977 2.359 1.00 0.00 WT1 H +ATOM 624 H2 TIP3W4809 15.065 2.796 1.789 1.00 0.00 WT1 H +ATOM 625 OH2 TIP3W6240 3.080 0.949 11.788 1.00 0.00 WT1 O +ATOM 626 H1 TIP3W6240 3.690 0.500 11.172 1.00 0.00 WT1 H +ATOM 627 H2 TIP3W6240 2.196 0.556 11.641 1.00 0.00 WT1 H +ATOM 628 OH2 TIP3W6671 0.897 12.813 20.940 1.00 0.00 WT1 O +ATOM 629 H1 TIP3W6671 1.234 13.577 21.489 1.00 0.00 WT1 H +ATOM 630 H2 TIP3W6671 1.110 12.083 21.442 1.00 0.00 WT1 H +ATOM 631 OH2 TIP3W7222 6.255 9.802 0.364 1.00 0.00 WT1 O +ATOM 632 H1 TIP3W7222 6.954 9.121 0.671 1.00 0.00 WT1 H +ATOM 633 H2 TIP3W7222 5.459 9.264 0.196 1.00 0.00 WT1 H +ATOM 634 OH2 TIP3W7479 6.140 3.669 3.704 1.00 0.00 WT1 O +ATOM 635 H1 TIP3W7479 6.732 3.837 2.949 1.00 0.00 WT1 H +ATOM 636 H2 TIP3W7479 6.807 3.408 4.378 1.00 0.00 WT1 H +ATOM 637 OH2 TIP3W7510 5.150 11.685 11.994 1.00 0.00 WT1 O +ATOM 638 H1 TIP3W7510 5.312 12.641 12.020 1.00 0.00 WT1 H +ATOM 639 H2 TIP3W7510 5.614 11.405 12.778 1.00 0.00 WT1 H +ATOM 640 OH2 TIP3W7563 5.196 19.304 15.315 1.00 0.00 WT1 O +ATOM 641 H1 TIP3W7563 5.227 20.213 14.942 1.00 0.00 WT1 H +ATOM 642 H2 TIP3W7563 5.252 18.720 14.569 1.00 0.00 WT1 H +ATOM 643 OH2 TIP3W7630 2.179 13.464 7.177 1.00 0.00 WT1 O +ATOM 644 H1 TIP3W7630 2.719 14.061 7.737 1.00 0.00 WT1 H +ATOM 645 H2 TIP3W7630 1.640 13.021 7.843 1.00 0.00 WT1 H +ATOM 646 OH2 TIP3W7631 1.926 21.439 17.027 1.00 0.00 WT1 O +ATOM 647 H1 TIP3W7631 2.672 21.817 16.545 1.00 0.00 WT1 H +ATOM 648 H2 TIP3W7631 2.398 20.912 17.662 1.00 0.00 WT1 H +ATOM 649 OH2 TIP3W7707 0.688 2.781 7.114 1.00 0.00 WT1 O +ATOM 650 H1 TIP3W7707 1.488 3.190 6.703 1.00 0.00 WT1 H +ATOM 651 H2 TIP3W7707 0.053 3.429 6.930 1.00 0.00 WT1 H +ATOM 652 OH2 TIP3W7985 0.449 7.366 9.140 1.00 0.00 WT1 O +ATOM 653 H1 TIP3W7985 0.202 6.479 9.095 1.00 0.00 WT1 H +ATOM 654 H2 TIP3W7985 0.796 7.563 8.256 1.00 0.00 WT1 H +ATOM 655 OH2 TIP3W8023 0.913 12.320 0.937 1.00 0.00 WT1 O +ATOM 656 H1 TIP3W8023 0.623 11.700 0.268 1.00 0.00 WT1 H +ATOM 657 H2 TIP3W8023 1.290 11.784 1.628 1.00 0.00 WT1 H +ATOM 658 OH2 TIP3W8029 7.889 16.997 14.360 1.00 0.00 WT1 O +ATOM 659 H1 TIP3W8029 7.935 17.181 13.358 1.00 0.00 WT1 H +ATOM 660 H2 TIP3W8029 8.602 17.562 14.734 1.00 0.00 WT1 H +ATOM 661 OH2 TIP3W8046 3.230 22.882 11.736 1.00 0.00 WT1 O +ATOM 662 H1 TIP3W8046 3.601 21.950 11.670 1.00 0.00 WT1 H +ATOM 663 H2 TIP3W8046 2.861 22.992 10.853 1.00 0.00 WT1 H +ATOM 664 OH2 TIP3W8064 4.620 22.335 7.130 1.00 0.00 WT1 O +ATOM 665 H1 TIP3W8064 3.754 22.591 7.590 1.00 0.00 WT1 H +ATOM 666 H2 TIP3W8064 5.178 22.349 7.907 1.00 0.00 WT1 H +ATOM 667 OH2 TIP3W8068 1.124 22.962 13.514 1.00 0.00 WT1 O +ATOM 668 H1 TIP3W8068 1.837 22.901 12.860 1.00 0.00 WT1 H +ATOM 669 H2 TIP3W8068 0.685 23.799 13.310 1.00 0.00 WT1 H +ATOM 670 OH2 TIP3W8364 8.561 10.924 16.881 1.00 0.00 WT1 O +ATOM 671 H1 TIP3W8364 7.916 11.188 16.202 1.00 0.00 WT1 H +ATOM 672 H2 TIP3W8364 8.309 10.008 17.123 1.00 0.00 WT1 H +ATOM 673 OH2 TIP3W8403 4.751 19.009 2.814 1.00 0.00 WT1 O +ATOM 674 H1 TIP3W8403 4.754 18.978 3.760 1.00 0.00 WT1 H +ATOM 675 H2 TIP3W8403 5.300 18.306 2.612 1.00 0.00 WT1 H +ATOM 676 OH2 TIP3W8411 3.406 0.117 14.493 1.00 0.00 WT1 O +ATOM 677 H1 TIP3W8411 3.348 0.244 13.546 1.00 0.00 WT1 H +ATOM 678 H2 TIP3W8411 4.378 0.190 14.724 1.00 0.00 WT1 H +ATOM 679 OH2 TIP3W8425 2.278 3.922 1.200 1.00 0.00 WT1 O +ATOM 680 H1 TIP3W8425 2.701 3.392 0.560 1.00 0.00 WT1 H +ATOM 681 H2 TIP3W8425 1.556 3.406 1.415 1.00 0.00 WT1 H +ATOM 682 OH2 TIP3W8441 6.246 21.216 13.564 1.00 0.00 WT1 O +ATOM 683 H1 TIP3W8441 7.127 21.533 13.794 1.00 0.00 WT1 H +ATOM 684 H2 TIP3W8441 5.802 22.075 13.455 1.00 0.00 WT1 H +ATOM 685 OH2 TIP3W8466 5.348 15.459 5.988 1.00 0.00 WT1 O +ATOM 686 H1 TIP3W8466 4.942 16.211 6.465 1.00 0.00 WT1 H +ATOM 687 H2 TIP3W8466 4.964 14.679 6.422 1.00 0.00 WT1 H +ATOM 688 OH2 TIP3W8468 1.312 13.577 13.829 1.00 0.00 WT1 O +ATOM 689 H1 TIP3W8468 1.594 13.350 12.963 1.00 0.00 WT1 H +ATOM 690 H2 TIP3W8468 0.905 14.443 13.634 1.00 0.00 WT1 H +ATOM 691 OH2 TIP3W8491 10.395 21.375 22.397 1.00 0.00 WT1 O +ATOM 692 H1 TIP3W8491 10.900 20.680 22.794 1.00 0.00 WT1 H +ATOM 693 H2 TIP3W8491 10.682 22.154 22.828 1.00 0.00 WT1 H +ATOM 694 OH2 TIP3W8528 6.013 16.085 3.326 1.00 0.00 WT1 O +ATOM 695 H1 TIP3W8528 6.016 16.035 4.292 1.00 0.00 WT1 H +ATOM 696 H2 TIP3W8528 5.249 15.516 3.046 1.00 0.00 WT1 H +ATOM 697 OH2 TIP3W8534 2.184 22.110 9.500 1.00 0.00 WT1 O +ATOM 698 H1 TIP3W8534 1.913 21.297 9.998 1.00 0.00 WT1 H +ATOM 699 H2 TIP3W8534 1.389 22.233 8.964 1.00 0.00 WT1 H +ATOM 700 OH2 TIP3W8536 3.207 13.979 17.772 1.00 0.00 WT1 O +ATOM 701 H1 TIP3W8536 3.947 14.082 18.373 1.00 0.00 WT1 H +ATOM 702 H2 TIP3W8536 2.585 14.685 17.921 1.00 0.00 WT1 H +ATOM 703 OH2 TIP3W8548 13.639 16.098 5.269 1.00 0.00 WT1 O +ATOM 704 H1 TIP3W8548 14.099 15.394 4.872 1.00 0.00 WT1 H +ATOM 705 H2 TIP3W8548 12.755 15.724 5.343 1.00 0.00 WT1 H +ATOM 706 OH2 TIP3W8556 1.981 16.635 18.663 1.00 0.00 WT1 O +ATOM 707 H1 TIP3W8556 1.921 17.181 19.529 1.00 0.00 WT1 H +ATOM 708 H2 TIP3W8556 2.656 17.117 18.156 1.00 0.00 WT1 H +ATOM 709 OH2 TIP3W8760 13.457 20.491 6.545 1.00 0.00 WT1 O +ATOM 710 H1 TIP3W8760 13.544 19.713 6.959 1.00 0.00 WT1 H +ATOM 711 H2 TIP3W8760 13.199 20.170 5.601 1.00 0.00 WT1 H +ATOM 712 OH2 TIP3W8780 3.438 8.099 0.316 1.00 0.00 WT1 O +ATOM 713 H1 TIP3W8780 2.547 7.847 0.577 1.00 0.00 WT1 H +ATOM 714 H2 TIP3W8780 3.889 7.775 1.093 1.00 0.00 WT1 H +ATOM 715 OH2 TIP3W8801 9.016 15.690 9.485 1.00 0.00 WT1 O +ATOM 716 H1 TIP3W8801 9.158 14.769 9.701 1.00 0.00 WT1 H +ATOM 717 H2 TIP3W8801 8.537 15.554 8.652 1.00 0.00 WT1 H +ATOM 718 OH2 TIP3W8822 1.562 6.536 12.239 1.00 0.00 WT1 O +ATOM 719 H1 TIP3W8822 0.960 7.250 12.049 1.00 0.00 WT1 H +ATOM 720 H2 TIP3W8822 1.197 5.827 11.553 1.00 0.00 WT1 H +ATOM 721 OH2 TIP3W8829 1.314 9.385 7.173 1.00 0.00 WT1 O +ATOM 722 H1 TIP3W8829 1.333 8.706 6.444 1.00 0.00 WT1 H +ATOM 723 H2 TIP3W8829 2.056 9.953 6.980 1.00 0.00 WT1 H +ATOM 724 OH2 TIP3W8843 7.572 0.420 3.478 1.00 0.00 WT1 O +ATOM 725 H1 TIP3W8843 7.636 0.339 2.503 1.00 0.00 WT1 H +ATOM 726 H2 TIP3W8843 6.628 0.234 3.530 1.00 0.00 WT1 H +ATOM 727 OH2 TIP3W8845 1.133 7.080 5.078 1.00 0.00 WT1 O +ATOM 728 H1 TIP3W8845 1.201 7.102 4.137 1.00 0.00 WT1 H +ATOM 729 H2 TIP3W8845 0.358 6.549 5.302 1.00 0.00 WT1 H +ATOM 730 OH2 TIP3W8865 11.515 22.342 4.827 1.00 0.00 WT1 O +ATOM 731 H1 TIP3W8865 10.875 21.911 4.185 1.00 0.00 WT1 H +ATOM 732 H2 TIP3W8865 11.205 21.919 5.694 1.00 0.00 WT1 H +ATOM 733 OH2 TIP3W8869 5.279 5.755 11.457 1.00 0.00 WT1 O +ATOM 734 H1 TIP3W8869 4.504 5.333 10.967 1.00 0.00 WT1 H +ATOM 735 H2 TIP3W8869 5.564 4.986 12.019 1.00 0.00 WT1 H +ATOM 736 OH2 TIP3W8887 8.890 21.041 16.070 1.00 0.00 WT1 O +ATOM 737 H1 TIP3W8887 8.698 21.572 15.300 1.00 0.00 WT1 H +ATOM 738 H2 TIP3W8887 9.800 21.340 16.244 1.00 0.00 WT1 H +ATOM 739 OH2 TIP3W8895 6.000 11.283 22.324 1.00 0.00 WT1 O +ATOM 740 H1 TIP3W8895 5.866 12.057 22.939 1.00 0.00 WT1 H +ATOM 741 H2 TIP3W8895 5.863 11.634 21.452 1.00 0.00 WT1 H +ATOM 742 OH2 TIP3W8905 7.834 14.408 7.527 1.00 0.00 WT1 O +ATOM 743 H1 TIP3W8905 7.105 14.717 6.993 1.00 0.00 WT1 H +ATOM 744 H2 TIP3W8905 8.194 13.714 6.926 1.00 0.00 WT1 H +ATOM 745 OH2 TIP3W8931 5.667 11.812 19.542 1.00 0.00 WT1 O +ATOM 746 H1 TIP3W8931 5.647 12.743 19.497 1.00 0.00 WT1 H +ATOM 747 H2 TIP3W8931 5.889 11.629 18.618 1.00 0.00 WT1 H +ATOM 748 OH2 TIP3W8932 12.997 18.576 15.207 1.00 0.00 WT1 O +ATOM 749 H1 TIP3W8932 12.617 19.193 14.493 1.00 0.00 WT1 H +ATOM 750 H2 TIP3W8932 13.582 19.163 15.737 1.00 0.00 WT1 H +ATOM 751 OH2 TIP3W8935 0.675 11.574 10.952 1.00 0.00 WT1 O +ATOM 752 H1 TIP3W8935 1.597 11.546 10.574 1.00 0.00 WT1 H +ATOM 753 H2 TIP3W8935 0.265 12.150 10.339 1.00 0.00 WT1 H +ATOM 754 OH2 TIP3W8949 8.782 17.187 2.362 1.00 0.00 WT1 O +ATOM 755 H1 TIP3W8949 8.004 16.786 2.797 1.00 0.00 WT1 H +ATOM 756 H2 TIP3W8949 9.140 16.422 1.970 1.00 0.00 WT1 H +ATOM 757 OH2 TIP3W8956 2.113 6.516 21.893 1.00 0.00 WT1 O +ATOM 758 H1 TIP3W8956 2.170 5.576 22.160 1.00 0.00 WT1 H +ATOM 759 H2 TIP3W8956 2.446 6.949 22.707 1.00 0.00 WT1 H +ATOM 760 OH2 TIP3W8977 2.583 16.123 12.046 1.00 0.00 WT1 O +ATOM 761 H1 TIP3W8977 3.491 16.508 12.059 1.00 0.00 WT1 H +ATOM 762 H2 TIP3W8977 2.312 16.312 12.887 1.00 0.00 WT1 H +ATOM 763 OH2 TIP3W8988 2.246 20.883 4.995 1.00 0.00 WT1 O +ATOM 764 H1 TIP3W8988 1.611 20.097 4.885 1.00 0.00 WT1 H +ATOM 765 H2 TIP3W8988 3.079 20.473 5.195 1.00 0.00 WT1 H +ATOM 766 OH2 TIP3W9082 8.156 17.564 11.520 1.00 0.00 WT1 O +ATOM 767 H1 TIP3W9082 8.355 18.345 10.921 1.00 0.00 WT1 H +ATOM 768 H2 TIP3W9082 8.334 16.820 10.874 1.00 0.00 WT1 H +ATOM 769 OH2 TIP3W9096 2.915 14.197 3.393 1.00 0.00 WT1 O +ATOM 770 H1 TIP3W9096 2.155 14.414 3.916 1.00 0.00 WT1 H +ATOM 771 H2 TIP3W9096 2.719 13.333 3.011 1.00 0.00 WT1 H +ATOM 772 OH2 TIP3W9226 8.578 0.832 6.351 1.00 0.00 WT1 O +ATOM 773 H1 TIP3W9226 7.928 0.530 5.693 1.00 0.00 WT1 H +ATOM 774 H2 TIP3W9226 8.563 1.801 6.335 1.00 0.00 WT1 H +ATOM 775 OH2 TIP3W9241 7.287 10.172 13.815 1.00 0.00 WT1 O +ATOM 776 H1 TIP3W9241 6.631 9.473 14.077 1.00 0.00 WT1 H +ATOM 777 H2 TIP3W9241 8.119 9.669 13.852 1.00 0.00 WT1 H +ATOM 778 OH2 TIP3W9250 3.347 10.487 19.814 1.00 0.00 WT1 O +ATOM 779 H1 TIP3W9250 2.792 10.955 19.188 1.00 0.00 WT1 H +ATOM 780 H2 TIP3W9250 4.264 10.639 19.456 1.00 0.00 WT1 H +END diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt new file mode 100644 index 0000000000..2b550b6309 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt @@ -0,0 +1,52 @@ +# file "spce.lt" +# +# H1 H2 +# \ / +# O + +SPCE { + + write_once("In Init") { + # -- Default styles (for solo "SPCE" water) -- + units real + atom_style full + # (Hybrid force fields were not necessary but are used for portability.) + pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 + bond_style hybrid harmonic + angle_style hybrid harmonic + kspace_style pppm 0.0001 + pair_modify mix arithmetic + } + + write("Data Atoms") { + $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 + $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 + $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590 + } + + write_once("Data Masses") { + @atom:O 15.9994 + @atom:H 1.008 + } + + write("Data Bonds") { + $bond:OH1 @bond:OH $atom:O $atom:H1 + $bond:OH2 @bond:OH $atom:O $atom:H2 + } + + write("Data Angles") { + $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 + } + + write_once("In Settings") { + bond_coeff @bond:OH harmonic 1000.0 1.0 + angle_coeff @angle:HOH harmonic 1000.0 109.47 + pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 + pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058 + group spce type @atom:O @atom:H + fix fSHAKE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH + # (Remember to "unfix" fSHAKE during minimization.) + } + +} # end of definition of "SPCE" water molecule type + diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/system.lt new file mode 100644 index 0000000000..274d8aeb11 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/system.lt @@ -0,0 +1,16 @@ +import "spce.lt" + +wat = new SPCE [260] + + + + + + + +# Open up the PDB file to count the number of water molecules inside. (Or just +# divide the number of atoms by 3). Put that in between the brackets ("[260]") +# +# The command above does not set the positions of the atoms. +# So they will have to be loaded later from a PDB or an XYZ file. +# (For example, using "moltemplate.sh -pdb solvate.pdb system.lt") diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt new file mode 100644 index 0000000000..4cbf67fc2d --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt @@ -0,0 +1,49 @@ +################################################## +# Box of water +################################################## +# +# define the system being simulated: + +# ----- init section ----- + +include system.in.init + + +# ----- atom definition section ----- + +read_data system.data + + +# ----- settings section ----- + +include system.in.settings + +# Load the atom coordinates: + +include "system.in.coords" + +# ----- run section ----- + + +# -- minimization protocol -- +# In general, it's always a good idea to minimize the system beforehand. +# fSHAKE was defined in system.in.settings. It is incompatible with "minimize". +unfix fSHAKE +minimize 1.0e-5 1.0e-7 100000 400000 +# Now read "system.in.settings" in order to redefine fSHAKE again: +include system.in.settings + +# -- simulation protocol -- + + +timestep 2.0 + +dump 1 all custom 100 traj_npt.lammpstrj id mol type x y z ix iy iz +fix fxnpt all npt temp 300.0 300.0 100.0 aniso 1.0 1.0 1000.0 drag 1.0 + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo 100 + +run 20000 + +write_restart system_after_npt.rst diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt new file mode 100644 index 0000000000..ed2d026c4f --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt @@ -0,0 +1,67 @@ +################################################## +# Box of water +################################################## +# +# define the system being simulated: + +# -- init section -- +include system.in.init + +# ------------------------ Atom Definition Section -------------- + +# Normally, I would minimize the system and equilibrate the system at constant +# pressure and temperature beforehand. If you run lammps with "run.in.npt", +# it will generate a restart file "system_after_npt.rst" with reasonable +# coordinates at that temperature and pressure. Then we could load it now: +# +#read_restart system_after_npt.rst +# +# Unfortunately the LAMMPS "read_restart" command has been undependable over +# the past year (2012), and I feel it is safer to remove it from the examples. +# Instead, for this example, I just read the raw coordinates generated by +# moltemplate (and the default volume). (I get fewer questions this way.) +# However you should never run any liquid simulations at constant volume without +# pressure equilibration first. Hopefully in the future "read_restart" will +# work. Otherwise try "read_dump", "dump2data.py", or "restart2data". + +read_data system.data + +# ------------------------ Settings section --------------------- + +include system.in.settings + +# Load the atom coordinates: + +include "system.in.coords" + +# ------------------------ Run section ------------------------- + + +# -- minimization protocol -- + +# In general, it's always a good idea to minimize the system beforehand. +# fSHAKE was defined in system.in.settings. It is incompatible with "minimize". +unfix fSHAKE +minimize 1.0e-5 1.0e-7 100000 400000 +# Now read "system.in.settings" in order to redefine fSHAKE again: +include system.in.settings + +# -- simulation protocol -- + + +timestep 2.0 + +dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz +fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 + +thermo_style custom step temp pe etotal press vol epair ebond eangle +thermo 500 # time interval for printing out "thermo" data +#thermo_modify flush yes + +restart 100000 restart_nvt + +run 50000 + +write_restart system_after_nvt.rst + + diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_run.sh b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_run.sh new file mode 100755 index 0000000000..cf51fa8705 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_run.sh @@ -0,0 +1,33 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_linux" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_linux -i run.in.npt # minimization and simulation at constant pressure + +# or + +lmp_linux -i run.in.nvt # minimization and simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation are ignored when beginning the simulation at constant volume. +# This can be fixed. Read "run.in.nvt" for equilibration instructions.) + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_linux -i run.in.npt +# or +#mpirun -np 4 lmp_linux -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_setup.sh new file mode 100755 index 0000000000..3a08212692 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_setup.sh @@ -0,0 +1,23 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -atomstyle full system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Cl.jpg b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Cl.jpg new file mode 100644 index 0000000000..5261bedc2c Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Cl.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Na.jpg b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Na.jpg new file mode 100644 index 0000000000..78c4056f8c Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Na.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/for_visualization/psf_file_created_by_topotools/system.psf new file mode 100644 index 0000000000..d255bf3683 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/for_visualization/psf_file_created_by_topotools/system.psf @@ -0,0 +1,4257 @@ +PSF + + 1 !NTITLE + REMARKS VMD generated structure x-plor psf file + + 3016 !NATOM + 1 1 3 3 -0.847600 15.9994 0 + 2 1 4 4 0.423800 1.0080 0 + 3 1 4 4 0.423800 1.0080 0 + 4 2 3 3 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a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=100ps.jpg b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=100ps.jpg new file mode 100644 index 0000000000..220a717271 Binary files /dev/null and b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=100ps.jpg differ diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/ions.lt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/ions.lt new file mode 100644 index 0000000000..0e080db74c --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/ions.lt @@ -0,0 +1,60 @@ +# We define two molecule classes to represent Na+ and Cl- ions, respectively. +# This may seem like overkill since they both only consist of one atom each. + + +# Note: Monovalent ion parameters for Ewald and SPC/E water +# are from: Joung & Cheatham JPCB (2008) +# These Lennard Jones parameters match the parameters for ions +# in SPC/E water in the "frcmod.ionsjc_spce" file distributed +# with Amber (the 2010 version). + + +NaIon { + write_once("In Settings") { + pair_coeff @atom:Na @atom:Na lj/charmm/coul/long 0.3526418 1.212 + } + + write_once("Data Masses") { + @atom:Na 22.9898 + } + + # assumes "full" atom style + write("Data Atoms") { + $atom:Na $mol @atom:Na 1.0 0.00000 0.00000 0.000000 + } +} # NaIon + + +ClIon { + write_once("In Settings") { + pair_coeff @atom:Cl @atom:Cl lj/charmm/coul/long 0.0127850 2.711 + } + + write_once("Data Masses") { + @atom:Cl 35.453 + } + + # assumes "full" atom style + write("Data Atoms") { + $atom:Cl $mol @atom:Cl -1.0 0.00000 0.00000 0.000000 + } +} # ClIon + + +write_once("In Init") { + # -- Default styles for ions -- + units real + atom_style full + # (Hybrid force fields were not necessary but are used for portability.) + pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 + kspace_style pppm 0.0001 + pair_modify mix arithmetic +} + +# Optional: Define a group named "ions" consisting of either Na or Cl ions. +write_once("In Settings") { + group ionNa type @atom:NaIon/Na @atom:NaIon/Na + group ionCl type @atom:ClIon/Cl @atom:ClIon/Cl + group ions type @atom:NaIon/Na @atom:ClIon/Cl +} + diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/spce.lt new file mode 100644 index 0000000000..2b550b6309 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/spce.lt @@ -0,0 +1,52 @@ +# file "spce.lt" +# +# H1 H2 +# \ / +# O + +SPCE { + + write_once("In Init") { + # -- Default styles (for solo "SPCE" water) -- + units real + atom_style full + # (Hybrid force fields were not necessary but are used for portability.) + pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 + bond_style hybrid harmonic + angle_style hybrid harmonic + kspace_style pppm 0.0001 + pair_modify mix arithmetic + } + + write("Data Atoms") { + $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 + $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 + $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590 + } + + write_once("Data Masses") { + @atom:O 15.9994 + @atom:H 1.008 + } + + write("Data Bonds") { + $bond:OH1 @bond:OH $atom:O $atom:H1 + $bond:OH2 @bond:OH $atom:O $atom:H2 + } + + write("Data Angles") { + $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 + } + + write_once("In Settings") { + bond_coeff @bond:OH harmonic 1000.0 1.0 + angle_coeff @angle:HOH harmonic 1000.0 109.47 + pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 + pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058 + group spce type @atom:O @atom:H + fix fSHAKE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH + # (Remember to "unfix" fSHAKE during minimization.) + } + +} # end of definition of "SPCE" water molecule type + diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/system.lt new file mode 100644 index 0000000000..f43f4263e8 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/system.lt @@ -0,0 +1,52 @@ +import "spce.lt" # <- This defines the SPCE water molecule. This file is + # located in the "common" directory. You can either copy it + # here, or (preferably), you can define a MOLTEMPLATE_PATH + # environment variable and point it to "common". + # (as explained in the installation section of the manual). + +import "ions.lt" # <- This defines the ions "NaIon" and "ClIon". + +# Periodic boundary conditions: +write_once("Data Boundary") { + 0.0 34.50 xlo xhi + 0.0 34.50 ylo yhi + 0.0 34.50 zlo zhi +} + + +# The next command generates a (rather dense) cubic lattice with +# spacing 3.45 Angstroms. (The pressure must be equilibrated later.) + +wat = new SPCE [10].move(0.00, 0.00, 3.45) + [10].move(0.00, 3.45, 0.00) + [10].move(3.45, 0.00, 0.00) + +# We now create a 2x2x2 lattice of Na+ and Cl- ions: + +na = new NaIon [2].move(0,0,17.25) + [2].move(0,17.25,0) + [2].move(17.25,0,0) + + +cl = new ClIon [2].move(0,0,17.25) + [2].move(0,17.25,0) + [2].move(17.25,0,0) + +na[*][*][*].move(5.175,5.175,5.6) +cl[*][*][*].move(12.075,12.075,12.5) + +# (The (5.175,5.175,5.175) and (12.075,12.075,12.075) translational shifts +# prevent the Na and Cl ions from overlapping +# with the water molecules or each other.) + + +# Comment: Fortunately the ions and the water in this example share the +# same force-field styles (so their was no need to use "hybrid" styles). +# If this were not the case, you might need to add something like this. +# +# write_once("In Init") { +# # -- Styles for the combined system (overrides earlier settings) -- +# pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 NEWPAIRSTYLE +# bond_style hybrid harmonic NEWBONDSTYLE +# angle_style hybrid harmonic NEWANGLESTYLE +# } diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.npt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.npt new file mode 100644 index 0000000000..b129469a88 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.npt @@ -0,0 +1,38 @@ +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + + +# -- minimization protocol -- + +# Note: The minimization step is not necessary in this example. However +# in general, it's always a good idea to minimize the system beforehand. +# fSHAKE was defined in system.in.settings. It is incompatible with "minimize". +unfix fSHAKE +minimize 1.0e-5 1.0e-7 100000 400000 +# Now read "system.in.settings" in order to redefine fSHAKE again: +include system.in.settings + +# -- simulation protocol -- + + +timestep 2.0 +dump 1 all custom 100 traj_npt.lammpstrj id mol type x y z ix iy iz +fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 + +thermo 100 +#thermo_modify flush yes + +run 20000 + +write_restart system_after_npt.rst diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt new file mode 100644 index 0000000000..b23a288c47 --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt @@ -0,0 +1,61 @@ +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + + +# Normally, I would minimize the system and equilibrate the system at constant +# pressure and temperature beforehand. If you run lammps with "run.in.npt", +# it will generate a restart file "system_after_npt.rst" with reasonable +# coordinates at that temperature and pressure. Then we could load it now: +# +#read_restart system_after_npt.rst +# +# Unfortunately the LAMMPS "read_restart" command has been undependable over +# the past year (2012), and I feel it is safer to remove it from the examples. +# Instead, for this example, I just read the raw coordinates generated by +# moltemplate (and the default volume). (I get fewer questions this way.) +# However you should never run any liquid simulations at constant volume without +# pressure equilibration first. Hopefully in the future "read_restart" will +# work. Until then, try "read_dump", "dump2data.py", or "restart2data". + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- + + +# -- minimization protocol -- + +# Note: The minimization step is not necessary in this example. However +# in general, it's always a good idea to minimize the system beforehand. +# fSHAKE was defined in system.in.settings. It is incompatible with "minimize". +unfix fSHAKE +minimize 1.0e-5 1.0e-7 100000 400000 +# Now read "system.in.settings" in order to redefine fSHAKE again: +include system.in.settings + +# -- simulation protocol -- + + + +timestep 2.0 +dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz +fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 + + +thermo 500 +#thermo_modify flush yes + + +#restart 100000 restart_nvt + +run 50000 + +write_restart system_after_nvt.rst + + diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/README.TXT b/tools/moltemplate/examples/silly/pyramids_vs_gravity/README.TXT new file mode 100644 index 0000000000..76caac02cc --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/README.TXT @@ -0,0 +1,22 @@ + Description: + +This is a simulation of pyramid-shaped objects resting on an immobile surface +(resembling graphene). Each pyramid is built from spherical particles stacked +like cannon-balls, or stacked fruit. Ordinarily, the stack does not move +because the particles at the ground layer are immobilized. However, +given an initial (small) perturbation the pyramids collapse in an avalanche. + +(In this example, the perturbation is due to shock because we (intentionally) + did not minimize the system before starting the simulation. This shock + causes an avalanche to occur approximately 5000 timesteps later.) + +The particles roll down the pyramid and bounce off the "ground". The bouncing +is due to a repulsive external force which is added artificially. +(See the "run.in" file.) The simulation looks weird without something +to bounce off of. So I added a graphene surface at the bottom as scenery. +(It does not exert any force on the atoms.) + +(Random comment: This could be a fun example to illustrate the Boltzmann + distribution. Because there is no damping, in a small region, the particle + heights should eventually approach the Boltzmann distribution for some + suitable temperature.) diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_VMD_graphene.txt b/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_VMD_graphene.txt new file mode 100644 index 0000000000..096674f7ff --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_VMD_graphene.txt @@ -0,0 +1,28 @@ + ------- A note on building the graphene sheet in VMD: ------ + +Probably you can ignore these instructions. +These instructions are not necessary for this example to run. + +This example contains several pyramid shaped objects resting on a surface +made of graphene. The instructions in this file explain how to build the +graphene (representing the "ground") using VMD instead of with moltemplate. + Why do this? +VMD can create graphene sheets with bonds connecting neighboring carbon atoms, +(which looks more pretty). However, as of 2013-4-29, moltemplate currently +can not generate these bonds. It does not matter physically in this case, +because the graphene sheet used here does not move. It is only used as +scenery, to graphically represent the ground surface. + +Select "Extensions"->"Modeling"->"Carbon Nanotube Builder" + Build a graphene sheet of size 39.8 x 39.8 (units: nm) + 400.3358398 399.876008 + (try to use a size compatible with the periodic boundaries) +Select "Extensions"->"Tk Console", and type + display backgroundgradient on + +Note: If you want to do this, before you run moltemplate, you may want to delete + the sections of the "system.lt" file (located in "moltemplate_files") + which define the graphene wall. Instead create the graphene data file + in VMD. You will have to manually merge the data file for graphene + with the data file for the pyramids created by moltemplate, + (taking care to avoid overlapping atom-id numbers). diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_setup.sh b/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_setup.sh new file mode 100755 index 0000000000..acc5fbbaad --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_setup.sh @@ -0,0 +1,23 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_visualize.txt b/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_visualize.txt new file mode 100644 index 0000000000..10198fc92f --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_visualize.txt @@ -0,0 +1,76 @@ + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + To shift the box by a fraction in the x direction (for example) + do this: + + pbc wrap -compound res -all -shiftcenterrel {-0.50 -0.52 0.0 } + pbc box -shiftcenterrel {-0.50 -0.52 0.0 } + + # Alternately if you have a solute whose atoms are all of type 1, + # then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=04800steps_LR.jpg b/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=04800steps_LR.jpg new file mode 100644 index 0000000000..dc010258f0 Binary files /dev/null and b/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=04800steps_LR.jpg differ diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=12200steps_LR.jpg b/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=12200steps_LR.jpg new file mode 100644 index 0000000000..53dc98f3e8 Binary files /dev/null and b/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=12200steps_LR.jpg differ diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=33000steps_LR.jpg b/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=33000steps_LR.jpg new file mode 100644 index 0000000000..ba07b25372 Binary files /dev/null and b/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=33000steps_LR.jpg differ diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/README.sh b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/README.sh new file mode 100644 index 0000000000..365ab9fb03 --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/README.sh @@ -0,0 +1,15 @@ +# This directory contains moltemplate files for the "Pyramids of Giza" example. +# (Note: the ground lattice work that appears in some images was not generated +# by moltemplate. Moltemplate can not currently create bonded periodic +# structures as of 2013-4-04. Those were generated by topotools.) +# +# To run moltemplate, use: + +moltemplate.sh system.lt + +# This will generate:system.data, system.in, system.in.init, system.in.settings +# +# The output_ttree/ directory will contain files like "Data Atoms", "Data Bonds" +# which contain the corresponding structures of the system.data file. +# (This might make it slightly easier to combine them with atom data and +# bond data generated by other programs, such as topotools, for example.) diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/graphene.lt b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/graphene.lt new file mode 100644 index 0000000000..3b3e21333f --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/graphene.lt @@ -0,0 +1,61 @@ +# This file contains a unit cell for building graphene and nanotubes +# +# +# The 4AtomRectCellXY "molecule" defined below is a reactangular unit cell +# for hexagonal tesselations in 2-dimensions. (See "graphene_unit_cell.jpg") +# Surfaces constructed with this unit cell can be flat or curved into tubes. +# The distance between nearest-neighbor carbon atoms (ie the length of a +# carbon-carbon bond) is equal to "d" which I set to 1.42 Angstroms. +# +# d = length of each hexagon's side = 1.42 Angstroms +# L = length of each hexagon = 2*d = 2.84 Angstroms +# W = width of each hexagon = 2*d*sqrt(3)/2 = 2.4595121467478056 Angstroms +# 2w = width of hexagon rows = 3*l = 4.26 Angstroms +# +# Consequently, the Lattice-cell vectors for singe-layer graphene are: +# (2.4595121467478, 0, 0) (aligned with X axis) +# (0, 4.26, 0) (aligned with Y axis) +# So, to build a sheet of graphite, you could use: +# sheet = new Graphene/4AtomRectCellXY [10].move(2.4595121467478, 0, 0) +# [10].move(0, 4.26, 0) + + + + +Graphene { + + 4AtomRectCellXY + { + # atomID molID atomType charge x y z + write("Data Atoms") { + $atom:C11 $mol:... @atom:../C 0.0 0.61487803668695 0.71 0.0 + $atom:C21 $mol:... @atom:../C 0.0 1.84463411006085 1.42 0.0 + $atom:C12 $mol:... @atom:../C 0.0 0.61487803668695 3.55 0.0 + $atom:C22 $mol:... @atom:../C 0.0 1.84463411006085 2.84 0.0 + } + } + + # Now define properties of the Carbon graphene atom + + write_once("In Init") { + pair_style hybrid lj/cut 9.0 + } + + write_once("Data Masses") { + @atom:C 12.0 + } + + write_once("In Settings") { + # i j epsilon sigma + pair_coeff @atom:C @atom:C lj/cut 0.068443 3.407 + + # These Lennard-Jones parameters come from + # R. Saito, R. Matsuo, T. Kimura, G. Dresselhaus, M.S. Dresselhaus, + # Chem Phys Lett, 348:187 (2001) + + # Define a group consisting of only carbon atoms in graphene molecules + group gGraphene type @atom:C + } + +} # Graphene + diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/graphene_wall.lt b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/graphene_wall.lt new file mode 100644 index 0000000000..759f0f5d06 --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/graphene_wall.lt @@ -0,0 +1,21 @@ +import "graphene.lt" + +# -------------- graphene sheet ----------------- + +# Notes: +# Hexagonal lattice with: +# l = length of each hexagonal side = 1.42 Angstroms +# L = length of each hexagon = 2*l = 2.84 Angstroms +# W = width of each hexagon = 2*l*sqrt(3)/2 ~= 2.4595121467478 Angstroms +# 2w = width of hexagon rows = 3.0*l = 4.26 Angstroms + + +GrapheneWall { + + unitcells = new Graphene/4AtomRectCellXY [163].move(2.456, 0, 0) + [94].move(0, 4.254, 0) + + # (Note: I fudged the spacing slightly to make it line up better with the + # lattice spacing for graphene generated by VMD's graphene builder.) +} + diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/pyramids.lt b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/pyramids.lt new file mode 100644 index 0000000000..7585b4ce0c --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/pyramids.lt @@ -0,0 +1,290 @@ +# Brick is a very simple molecule containing one "atom". +# "ImmobileBrick" and "GoldBrick" are identical to "Brick" but are +# given different atom types. (This makes it easier to put them in +# different groups and apply different LAMMPS "fixes" to them.) + +Brick { + + # atomID molID atomType charge x y z + write("Data Atoms") { + $atom $mol @atom 0.0 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom 1.0 + } + + write_once("In Settings") { + # U(r) = 4*epsilon_ij*((sigma_ij/r)^12 - (sigma_ij/r)^6) + # + # i j eps sig + pair_coeff @atom @atom lj/cut 1.0 0.8908987181403393 + } + + write_once("In Settings") { + group gMobile type @atom + # (Atoms of this type belong to the "gMobile" group) + } + + write_once("In Init") { + atom_style full + units lj + pair_style lj/cut 1.0 + } +} + + + +#We want to stack "Brick"s the same way a green-grocer sometimes stack apples: +#Place the apples at the base an square lattice of apples at the base. +#The apples in the next layer up are placed in between the 4 apples beneath them. +#Each new layer is smaller and placed above the previous layer at a height +#of sigma / sqrt(2), where "sigma" is the diameter of each spherical "Brick". +#We will artificially hold the apples at the base in place +#(to keep the entire stack from collapsing). +# +# The lines below were generated from the following python loop: +# +#from math import * +#N=50 +#s=1.0 +#for i in range(0,N): +# print(" layer"+str(i)+" = new Brick.move("+str(-(N-(i+1))*s*0.5)+","+ +# str(-(N-(i+1))*s*0.5)+","+str(i*s/sqrt(2))+") ["+str(N-i)+"].move("+ +# str(s)+",0,0) ["+str(N-i)+"].move(0,"+str(s)+",0)") + + +PyramidKhufu { + layer0 = new ImmobileBrick.move(-24.5,-24.5,0.0) [50].move(1.0,0,0) [50].move(0,1.0,0) + layer1 = new Brick.move(-24.0,-24.0,0.707106781187) [49].move(1.0,0,0) [49].move(0,1.0,0) + layer2 = new Brick.move(-23.5,-23.5,1.41421356237) [48].move(1.0,0,0) [48].move(0,1.0,0) + layer3 = new Brick.move(-23.0,-23.0,2.12132034356) [47].move(1.0,0,0) [47].move(0,1.0,0) + layer4 = new Brick.move(-22.5,-22.5,2.82842712475) [46].move(1.0,0,0) [46].move(0,1.0,0) + layer5 = new Brick.move(-22.0,-22.0,3.53553390593) [45].move(1.0,0,0) [45].move(0,1.0,0) + layer6 = new Brick.move(-21.5,-21.5,4.24264068712) [44].move(1.0,0,0) [44].move(0,1.0,0) + layer7 = new Brick.move(-21.0,-21.0,4.94974746831) [43].move(1.0,0,0) [43].move(0,1.0,0) + layer8 = new Brick.move(-20.5,-20.5,5.65685424949) [42].move(1.0,0,0) [42].move(0,1.0,0) + layer9 = new Brick.move(-20.0,-20.0,6.36396103068) [41].move(1.0,0,0) [41].move(0,1.0,0) + layer10 = new Brick.move(-19.5,-19.5,7.07106781187) [40].move(1.0,0,0) [40].move(0,1.0,0) + layer11 = new Brick.move(-19.0,-19.0,7.77817459305) [39].move(1.0,0,0) [39].move(0,1.0,0) + layer12 = new Brick.move(-18.5,-18.5,8.48528137424) [38].move(1.0,0,0) [38].move(0,1.0,0) + layer13 = new Brick.move(-18.0,-18.0,9.19238815543) [37].move(1.0,0,0) [37].move(0,1.0,0) + layer14 = new Brick.move(-17.5,-17.5,9.89949493661) [36].move(1.0,0,0) [36].move(0,1.0,0) + layer15 = new Brick.move(-17.0,-17.0,10.6066017178) [35].move(1.0,0,0) [35].move(0,1.0,0) + layer16 = new Brick.move(-16.5,-16.5,11.313708499) [34].move(1.0,0,0) [34].move(0,1.0,0) + layer17 = new Brick.move(-16.0,-16.0,12.0208152802) [33].move(1.0,0,0) [33].move(0,1.0,0) + layer18 = new Brick.move(-15.5,-15.5,12.7279220614) [32].move(1.0,0,0) [32].move(0,1.0,0) + layer19 = new Brick.move(-15.0,-15.0,13.4350288425) [31].move(1.0,0,0) [31].move(0,1.0,0) + layer20 = new Brick.move(-14.5,-14.5,14.1421356237) [30].move(1.0,0,0) [30].move(0,1.0,0) + layer21 = new Brick.move(-14.0,-14.0,14.8492424049) [29].move(1.0,0,0) [29].move(0,1.0,0) + layer22 = new Brick.move(-13.5,-13.5,15.5563491861) [28].move(1.0,0,0) [28].move(0,1.0,0) + layer23 = new Brick.move(-13.0,-13.0,16.2634559673) [27].move(1.0,0,0) [27].move(0,1.0,0) + layer24 = new Brick.move(-12.5,-12.5,16.9705627485) [26].move(1.0,0,0) [26].move(0,1.0,0) + layer25 = new Brick.move(-12.0,-12.0,17.6776695297) [25].move(1.0,0,0) [25].move(0,1.0,0) + layer26 = new Brick.move(-11.5,-11.5,18.3847763109) [24].move(1.0,0,0) [24].move(0,1.0,0) + layer27 = new Brick.move(-11.0,-11.0,19.091883092) [23].move(1.0,0,0) [23].move(0,1.0,0) + layer28 = new Brick.move(-10.5,-10.5,19.7989898732) [22].move(1.0,0,0) [22].move(0,1.0,0) + layer29 = new Brick.move(-10.0,-10.0,20.5060966544) [21].move(1.0,0,0) [21].move(0,1.0,0) + layer30 = new Brick.move(-9.5,-9.5,21.2132034356) [20].move(1.0,0,0) [20].move(0,1.0,0) + layer31 = new Brick.move(-9.0,-9.0,21.9203102168) [19].move(1.0,0,0) [19].move(0,1.0,0) + layer32 = new Brick.move(-8.5,-8.5,22.627416998) [18].move(1.0,0,0) [18].move(0,1.0,0) + layer33 = new Brick.move(-8.0,-8.0,23.3345237792) [17].move(1.0,0,0) [17].move(0,1.0,0) + layer34 = new Brick.move(-7.5,-7.5,24.0416305603) [16].move(1.0,0,0) [16].move(0,1.0,0) + layer35 = new Brick.move(-7.0,-7.0,24.7487373415) [15].move(1.0,0,0) [15].move(0,1.0,0) + layer36 = new Brick.move(-6.5,-6.5,25.4558441227) [14].move(1.0,0,0) [14].move(0,1.0,0) + layer37 = new Brick.move(-6.0,-6.0,26.1629509039) [13].move(1.0,0,0) [13].move(0,1.0,0) + layer38 = new Brick.move(-5.5,-5.5,26.8700576851) [12].move(1.0,0,0) [12].move(0,1.0,0) + layer39 = new Brick.move(-5.0,-5.0,27.5771644663) [11].move(1.0,0,0) [11].move(0,1.0,0) + layer40 = new GoldBrick.move(-4.5,-4.5,28.2842712475) [10].move(1.0,0,0) [10].move(0,1.0,0) + layer41 = new GoldBrick.move(-4.0,-4.0,28.9913780286) [9].move(1.0,0,0) [9].move(0,1.0,0) + layer42 = new GoldBrick.move(-3.5,-3.5,29.6984848098) [8].move(1.0,0,0) [8].move(0,1.0,0) + layer43 = new GoldBrick.move(-3.0,-3.0,30.405591591) [7].move(1.0,0,0) [7].move(0,1.0,0) + layer44 = new GoldBrick.move(-2.5,-2.5,31.1126983722) [6].move(1.0,0,0) [6].move(0,1.0,0) + layer45 = new GoldBrick.move(-2.0,-2.0,31.8198051534) [5].move(1.0,0,0) [5].move(0,1.0,0) + layer46 = new GoldBrick.move(-1.5,-1.5,32.5269119346) [4].move(1.0,0,0) [4].move(0,1.0,0) + layer47 = new GoldBrick.move(-1.0,-1.0,33.2340187158) [3].move(1.0,0,0) [3].move(0,1.0,0) + layer48 = new GoldBrick.move(-0.5,-0.5,33.941125497) [2].move(1.0,0,0) [2].move(0,1.0,0) + layer49 = new GoldBrick.move(0.0,0.0,34.6482322781) [1].move(1.0,0,0) [1].move(0,1.0,0) +} + + +PyramidKhafre { + layer0 = new ImmobileBrick.move(-23.5,-23.5,0.0) [48].move(1.0,0,0) [48].move(0,1.0,0) + layer1 = new Brick.move(-23.0,-23.0,0.707106781187) [47].move(1.0,0,0) [47].move(0,1.0,0) + layer2 = new Brick.move(-22.5,-22.5,1.41421356237) [46].move(1.0,0,0) [46].move(0,1.0,0) + layer3 = new Brick.move(-22.0,-22.0,2.12132034356) [45].move(1.0,0,0) [45].move(0,1.0,0) + layer4 = new Brick.move(-21.5,-21.5,2.82842712475) [44].move(1.0,0,0) [44].move(0,1.0,0) + layer5 = new Brick.move(-21.0,-21.0,3.53553390593) [43].move(1.0,0,0) [43].move(0,1.0,0) + layer6 = new Brick.move(-20.5,-20.5,4.24264068712) [42].move(1.0,0,0) [42].move(0,1.0,0) + layer7 = new Brick.move(-20.0,-20.0,4.94974746831) [41].move(1.0,0,0) [41].move(0,1.0,0) + layer8 = new Brick.move(-19.5,-19.5,5.65685424949) [40].move(1.0,0,0) [40].move(0,1.0,0) + layer9 = new Brick.move(-19.0,-19.0,6.36396103068) [39].move(1.0,0,0) [39].move(0,1.0,0) + layer10 = new Brick.move(-18.5,-18.5,7.07106781187) [38].move(1.0,0,0) [38].move(0,1.0,0) + layer11 = new Brick.move(-18.0,-18.0,7.77817459305) [37].move(1.0,0,0) [37].move(0,1.0,0) + layer12 = new Brick.move(-17.5,-17.5,8.48528137424) [36].move(1.0,0,0) [36].move(0,1.0,0) + layer13 = new Brick.move(-17.0,-17.0,9.19238815543) [35].move(1.0,0,0) [35].move(0,1.0,0) + layer14 = new Brick.move(-16.5,-16.5,9.89949493661) [34].move(1.0,0,0) [34].move(0,1.0,0) + layer15 = new Brick.move(-16.0,-16.0,10.6066017178) [33].move(1.0,0,0) [33].move(0,1.0,0) + layer16 = new Brick.move(-15.5,-15.5,11.313708499) [32].move(1.0,0,0) [32].move(0,1.0,0) + layer17 = new Brick.move(-15.0,-15.0,12.0208152802) [31].move(1.0,0,0) [31].move(0,1.0,0) + layer18 = new Brick.move(-14.5,-14.5,12.7279220614) [30].move(1.0,0,0) [30].move(0,1.0,0) + layer19 = new Brick.move(-14.0,-14.0,13.4350288425) [29].move(1.0,0,0) [29].move(0,1.0,0) + layer20 = new Brick.move(-13.5,-13.5,14.1421356237) [28].move(1.0,0,0) [28].move(0,1.0,0) + layer21 = new Brick.move(-13.0,-13.0,14.8492424049) [27].move(1.0,0,0) [27].move(0,1.0,0) + layer22 = new Brick.move(-12.5,-12.5,15.5563491861) [26].move(1.0,0,0) [26].move(0,1.0,0) + layer23 = new Brick.move(-12.0,-12.0,16.2634559673) [25].move(1.0,0,0) [25].move(0,1.0,0) + layer24 = new Brick.move(-11.5,-11.5,16.9705627485) [24].move(1.0,0,0) [24].move(0,1.0,0) + layer25 = new Brick.move(-11.0,-11.0,17.6776695297) [23].move(1.0,0,0) [23].move(0,1.0,0) + layer26 = new Brick.move(-10.5,-10.5,18.3847763109) [22].move(1.0,0,0) [22].move(0,1.0,0) + layer27 = new Brick.move(-10.0,-10.0,19.091883092) [21].move(1.0,0,0) [21].move(0,1.0,0) + layer28 = new Brick.move(-9.5,-9.5,19.7989898732) [20].move(1.0,0,0) [20].move(0,1.0,0) + layer29 = new Brick.move(-9.0,-9.0,20.5060966544) [19].move(1.0,0,0) [19].move(0,1.0,0) + layer30 = new Brick.move(-8.5,-8.5,21.2132034356) [18].move(1.0,0,0) [18].move(0,1.0,0) + layer31 = new Brick.move(-8.0,-8.0,21.9203102168) [17].move(1.0,0,0) [17].move(0,1.0,0) + layer32 = new Brick.move(-7.5,-7.5,22.627416998) [16].move(1.0,0,0) [16].move(0,1.0,0) + layer33 = new Brick.move(-7.0,-7.0,23.3345237792) [15].move(1.0,0,0) [15].move(0,1.0,0) + layer34 = new Brick.move(-6.5,-6.5,24.0416305603) [14].move(1.0,0,0) [14].move(0,1.0,0) + layer35 = new GoldBrick.move(-6.0,-6.0,24.7487373415) [13].move(1.0,0,0) [13].move(0,1.0,0) + layer36 = new GoldBrick.move(-5.5,-5.5,25.4558441227) [12].move(1.0,0,0) [12].move(0,1.0,0) + layer37 = new GoldBrick.move(-5.0,-5.0,26.1629509039) [11].move(1.0,0,0) [11].move(0,1.0,0) + layer38 = new GoldBrick.move(-4.5,-4.5,26.8700576851) [10].move(1.0,0,0) [10].move(0,1.0,0) + layer39 = new GoldBrick.move(-4.0,-4.0,27.5771644663) [9].move(1.0,0,0) [9].move(0,1.0,0) + layer40 = new GoldBrick.move(-3.5,-3.5,28.2842712475) [8].move(1.0,0,0) [8].move(0,1.0,0) + layer41 = new GoldBrick.move(-3.0,-3.0,28.9913780286) [7].move(1.0,0,0) [7].move(0,1.0,0) + layer42 = new GoldBrick.move(-2.5,-2.5,29.6984848098) [6].move(1.0,0,0) [6].move(0,1.0,0) + layer43 = new GoldBrick.move(-2.0,-2.0,30.405591591) [5].move(1.0,0,0) [5].move(0,1.0,0) + layer44 = new GoldBrick.move(-1.5,-1.5,31.1126983722) [4].move(1.0,0,0) [4].move(0,1.0,0) + layer45 = new GoldBrick.move(-1.0,-1.0,31.8198051534) [3].move(1.0,0,0) [3].move(0,1.0,0) + layer46 = new GoldBrick.move(-0.5,-0.5,32.5269119346) [2].move(1.0,0,0) [2].move(0,1.0,0) + layer47 = new GoldBrick.move(0.0,0.0,33.2340187158) [1].move(1.0,0,0) [1].move(0,1.0,0) +} + + +PyramidMenkaure { + layer0 = new ImmobileBrick.move(-9.0,-9.0,0.0) [19].move(1.0,0,0) [19].move(0,1.0,0) + layer1 = new Brick.move(-8.5,-8.5,0.707106781187) [18].move(1.0,0,0) [18].move(0,1.0,0) + layer2 = new Brick.move(-8.0,-8.0,1.41421356237) [17].move(1.0,0,0) [17].move(0,1.0,0) + layer3 = new Brick.move(-7.5,-7.5,2.12132034356) [16].move(1.0,0,0) [16].move(0,1.0,0) + layer4 = new Brick.move(-7.0,-7.0,2.82842712475) [15].move(1.0,0,0) [15].move(0,1.0,0) + layer5 = new Brick.move(-6.5,-6.5,3.53553390593) [14].move(1.0,0,0) [14].move(0,1.0,0) + layer6 = new Brick.move(-6.0,-6.0,4.24264068712) [13].move(1.0,0,0) [13].move(0,1.0,0) + layer7 = new Brick.move(-5.5,-5.5,4.94974746831) [12].move(1.0,0,0) [12].move(0,1.0,0) + layer8 = new Brick.move(-5.0,-5.0,5.65685424949) [11].move(1.0,0,0) [11].move(0,1.0,0) + layer9 = new Brick.move(-4.5,-4.5,6.36396103068) [10].move(1.0,0,0) [10].move(0,1.0,0) + layer10 = new Brick.move(-4.0,-4.0,7.07106781187) [9].move(1.0,0,0) [9].move(0,1.0,0) + layer11 = new Brick.move(-3.5,-3.5,7.77817459305) [8].move(1.0,0,0) [8].move(0,1.0,0) + layer12 = new Brick.move(-3.0,-3.0,8.48528137424) [7].move(1.0,0,0) [7].move(0,1.0,0) + layer13 = new Brick.move(-2.5,-2.5,9.19238815543) [6].move(1.0,0,0) [6].move(0,1.0,0) + layer14 = new Brick.move(-2.0,-2.0,9.89949493661) [5].move(1.0,0,0) [5].move(0,1.0,0) + layer15 = new Brick.move(-1.5,-1.5,10.6066017178) [4].move(1.0,0,0) [4].move(0,1.0,0) + layer16 = new Brick.move(-1.0,-1.0,11.313708499) [3].move(1.0,0,0) [3].move(0,1.0,0) + layer17 = new Brick.move(-0.5,-0.5,12.0208152802) [2].move(1.0,0,0) [2].move(0,1.0,0) + layer18 = new Brick.move(0.0,0.0,12.7279220614) [1].move(1.0,0,0) [1].move(0,1.0,0) +} + +PyramidQueens1 { + #layer0 = new ImmobileBrick.move(-3.5,-3.5,0.0) [8].move(1.0,0,0) [8].move(0,1.0,0) + #layer1 = new ImmobileBrick.move(-3.0,-3.0,0.707106781187) [7].move(1.0,0,0) [7].move(0,1.0,0) + #layer2 = new ImmobileBrick.move(-2.0,-2.0,1.41421356237) [5].move(1.0,0,0) [5].move(0,1.0,0) + #layer3 = new ImmobileBrick.move(-1.5,-1.5,2.12132034356) [4].move(1.0,0,0) [4].move(0,1.0,0) + #layer4 = new Brick.move(-0.5,-0.5,2.82842712475) [2].move(1.0,0,0) [2].move(0,1.0,0) + #layer5 = new Brick.move(0.0,0.0,3.53553390593) [1].move(1.0,0,0) [1].move(0,1.0,0) + + layer0 = new ImmobileBrick.move(-3.5,-3.5,0.0) [8].move(1.0,0,0) [8].move(0,1.0,0) + layer1 = new ImmobileBrick.move(-3.0,-3.0,0.707106781187) [7].move(1.0,0,0) [7].move(0,1.0,0) + layer2 = new ImmobileBrick.move(-2.0,-2.0,1.707106781187) [5].move(1.0,0,0) [5].move(0,1.0,0) + layer3 = new Brick.move(-1.5,-1.5,2.41421356237) [4].move(1.0,0,0) [4].move(0,1.0,0) + layer4 = new Brick.move(-0.5,-0.5,3.41421356237) [2].move(1.0,0,0) [2].move(0,1.0,0) + layer5 = new Brick.move(0.0,0.0,4.12132034356) [1].move(1.0,0,0) [1].move(0,1.0,0) +} + +PyramidQueens2 { + layer0 = new ImmobileBrick.move(-3.5,-3.5,0.0) [8].move(1.0,0,0) [8].move(0,1.0,0) + layer1 = new ImmobileBrick.move(-3.0,-3.0,0.707106781187) [7].move(1.0,0,0) [7].move(0,1.0,0) + layer2 = new ImmobileBrick.move(-2.0,-2.0,1.707106781187) [5].move(1.0,0,0) [5].move(0,1.0,0) + layer3 = new Brick.move(-1.5,-1.5,2.41421356237) [4].move(1.0,0,0) [4].move(0,1.0,0) + layer4 = new Brick.move(-0.5,-0.5,3.41421356237) [2].move(1.0,0,0) [2].move(0,1.0,0) + layer5 = new Brick.move(0.0,0.0,4.12132034356) [1].move(1.0,0,0) [1].move(0,1.0,0) +} + +PyramidQueens3 { + layer0 = new ImmobileBrick.move(-3.5,-3.5,0.0) [8].move(1.0,0,0) [8].move(0,1.0,0) + layer1 = new Brick.move(-3.0,-3.0,0.707106781187) [7].move(1.0,0,0) [7].move(0,1.0,0) + layer2 = new Brick.move(-2.5,-2.5,1.41421356237) [6].move(1.0,0,0) [6].move(0,1.0,0) + layer3 = new Brick.move(-2.0,-2.0,2.12132034356) [5].move(1.0,0,0) [5].move(0,1.0,0) + layer4 = new Brick.move(-1.5,-1.5,2.82842712475) [4].move(1.0,0,0) [4].move(0,1.0,0) + layer5 = new Brick.move(-1.0,-1.0,3.53553390593) [3].move(1.0,0,0) [3].move(0,1.0,0) + layer6 = new Brick.move(-0.5,-0.5,4.24264068712) [2].move(1.0,0,0) [2].move(0,1.0,0) + layer7 = new Brick.move(0.0,0.0,4.94974746831) [1].move(1.0,0,0) [1].move(0,1.0,0) +} + + + + +# "ImmobileBrick"s are identical to "Brick"s, +# except that they have a different atom type. +# We can define groups based on atom type +# and apply fixes to them. + +ImmobileBrick { + + # atomID molID atomType charge x y z + write("Data Atoms") { + $atom $mol @atom 0.0 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom 1.0 + } + + write_once("In Settings") { + # U(r) = 4*epsilon_ij*((sigma_ij/r)^12 - (sigma_ij/r)^6) + # + # i j eps sig + pair_coeff @atom @atom lj/cut 1.0 0.8908987181403393 + } + + write_once("In Settings") { + group gImmobile type @atom + # (Atoms of this type belong to the "gImmobile" group) + } + + write_once("In Init") { + atom_style full + units lj + pair_style hybrid lj/cut 1.0 + } +} + + + +GoldBrick { + + # atomID molID atomType charge x y z + write("Data Atoms") { + $atom $mol @atom 0.0 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom 1.0 + } + + write_once("In Settings") { + # U(r) = 4*epsilon_ij*((sigma_ij/r)^12 - (sigma_ij/r)^6) + # + # i j eps sig + pair_coeff @atom @atom lj/cut 1.0 0.8908987181403393 + } + + write_once("In Settings") { + group gMobile type @atom + # (Atoms of this type belong to the "gMobile" group) + } + + write_once("In Init") { + atom_style full + units lj + pair_style lj/cut 1.0 + } +} + diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/system.lt b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/system.lt new file mode 100644 index 0000000000..0c9c50ae9b --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/system.lt @@ -0,0 +1,80 @@ +# Description. +# This is a simulation of pyramid-like objects made of particles stacked +# and arranged like cannon-balls, or fruit-stands. Ordinarilly, the stack +# does not collapse because the particles at the ground layer are immobilized. +# However given an initial perterbation the pyramids collapse in an avalanche. +# (This can happen, for example when you do not minimize the system beforehand.) +# The particles roll down the pyramid and bounce off the "ground". The bouncing +# is due to a repulsive external force which is added artificially. +# (See the "run.in" file.) The simulation looks weird without something +# to bounce off of. So I added a graphene surface at the bottom as scenery. +# The ground does not serve any purpose except to look pretty. +# +# (Because there is no damping, I suspect that the distribution of heights of +# the particles in a small area should approach the Boltzmann distribution, +# if you run the simulation long enough.) + + +# ----------------- Pyramids: ----------------- + +import "pyramids.lt" + +# Move the pyramids into their locations in Giza (approximate) + +pyramidKhufu = new PyramidKhufu.move(210, 215, 1) +pyramidKhafre = new PyramidKhafre.move(150, 150, 1) +pyramidMenkaure = new PyramidMenkaure.move(105, 082, 1) +PyramidQueens1 = new PyramidQueens1.move(089, 059, 1) +PyramidQueens2 = new PyramidQueens2.move(100, 059, 1) +PyramidQueens3 = new PyramidQueens3.move(111, 059, 1) + + +# --------------- Scenery: -------------------- + +import "graphene_wall.lt" + +graphene_wall = new GrapheneWall + +write_once("In Settings") { + # Turn off all interactions with the graphene atoms by setting epsilon to 0. + # (We will use a different repulsive barrier to represent the ground instead.) + # These atoms are just "for show". epsilon sigma + pair_coeff @atom:Graphene/C @atom:Graphene/C lj/cut 0.00000 3.407 + + # Optional: Add the graphene atoms to the "gImmobile" group. Later freeze them + group gImmobile type @atom:Graphene/C +} + +# Unfortunately, the ground still looks kind of ugly because moltemplate does +# not yet know how to automatically connect nearby carbon atoms with C-C bonds +# (based on distance). (As of 2013-4-29, moltemplate is not good at +# generating crystalline objects containing explicit bonds.) +# If you want bonds between atoms, use VMD's "carbon-nanotube-builder plugin" +# (which creates data files with bonds) and then merge the two data files +# manually later. (This is not done here.) + + +# -------- override earlier settings ---------- + +write_once("In Init") { + # Override any earlier style settings + atom_style full + units lj + pair_style hybrid lj/cut 1.0 + bond_style none + angle_style none + dihedral_style none + improper_style none + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 0.0 +} + +# ------------ boundary conditions ------------ + +write_once("Data Boundary") { + -1.842033 398.493813 xlo xhi + -0.708994 399.167013 ylo yhi + 0.0 400.0 zlo zhi +} +# --------------------------------------------- + diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/run.in b/tools/moltemplate/examples/silly/pyramids_vs_gravity/run.in new file mode 100644 index 0000000000..4feec9ff4e --- /dev/null +++ b/tools/moltemplate/examples/silly/pyramids_vs_gravity/run.in @@ -0,0 +1,64 @@ +# -- Init Section -- + +include system.in.init +boundary p p f + +# -- Atom Definition Section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 0.0025 +dump 1 all custom 200 traj_nvt.lammpstrj id mol type x y z ix iy iz + +thermo_style custom step temp pe etotal +thermo 100 # time interval for printing out "thermo" data + +# ---- Set up the physical environment ---- + +# Add gravity: +fix fxGrav gMobile gravity 0.05 vector 0 0 -1 + +# Create a "ground" surface. +# This is a repulsive "wall" which particles can bounce off of: + +fix fxWall gMobile wall/lj126 zlo EDGE 1.0 0.8908987181403393 1.0 + + +# ---- Evolve the system: ---- + +# Evolve the (mobile) atoms using ordinary Newton's laws (NVE) + +fix fxNVE gMobile nve + + +# IF YOU WANT TO ADD DAMPING, THEN UNCOMMENT THE NEXT LINE: +#fix fxLan gMobile langevin 0.001 0.001 10000.0 48279 +# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve" +# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) +# This was not tested. + +# For efficient simulation in parallel, try using "fix balance": +# (This will adjust the spatial decomposition as the distribution of +# particles changes over time.) + +fix fxBalance gMobile balance 1000 xy 20 1.3 + +# Optional: Improve efficiency by omitting the calcuation of interactions +# between immobile atoms: + +neigh_modify exclude group gImmobile gImmobile + + +restart 50000 restart_nvt + +run 200000 + +write_restart system_after_nvt.rst + diff --git a/tools/moltemplate/examples/silly/sierpinski/README.TXT b/tools/moltemplate/examples/silly/sierpinski/README.TXT new file mode 100644 index 0000000000..6bc152b186 --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/README.TXT @@ -0,0 +1,45 @@ +NOTE: This example requires the "Al99.eam.alloy" file. + (It was not included in this directory because if its large size.) + As of 2012-11, I was able to obtain it here: + http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy + Copy it to the directory containing this README file. +------------------------------------------------------------------------ +3D fractal test + +Moltemplate is useful for building larger molecular structures from +smaller pieces. Although this simulation is of no scientific value, thiss +example illustrates how to build large (many-level) heirarchical objects +(Serpinski cubes) using moltemplate. (This is also called a "Menger Sponge".) + +The files in this directory demonstrate a way to build a periodic lattice of +3-dimensional Serpinski-cubes (with 3 levels of recursive self-similarity). + +In this example, the basic indivisible units are 4-atoms of Aluminum +(arranged in a cubic FCC unit-cell for bulk Aluminum). +This was an arbitrary choice. The resulting construct is not stable. +(But it makes pretty movies while collapsing.) + +To understand what is going on with this example, look at this file: + +./moltemplate_files/elegant_inefficient_version/serpinski_cubes.lt + +(This approach uses too much memory to be practical for large simulaions. +The version I actually use is here: ./moltemplate_files/serpinski_cubes.lt) + + --- To build the system --- + +Carry out the instructions in README_setup.sh, +to generate the LAMMPS DATA file and input scripts you need: +system.data, system.in.init, system.in.settings. +(The run.in script contains references to these files.) + + --- To run LAMMPS, try a command like: --- + +lmp_linux -i run.in + + or (if you have mpi installed) + +mpirun -np 4 lmp_linux -i run.in + +This will create an ordinary LAMMPS dump file you can visualize with VMD +traj.lammpstrj (See README_visualize.txt) diff --git a/tools/moltemplate/examples/silly/sierpinski/README_setup.sh b/tools/moltemplate/examples/silly/sierpinski/README_setup.sh new file mode 100755 index 0000000000..2af3d7372c --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/README_setup.sh @@ -0,0 +1,29 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh -atomstyle full system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # We will also need the "Al99.eam.alloy" file: + #cp -f Al99.eam.alloy ../ + # This file was downloaded from: + # http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy + + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/silly/sierpinski/README_visualize.txt b/tools/moltemplate/examples/silly/sierpinski/README_visualize.txt new file mode 100644 index 0000000000..019afc1444 --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/silly/sierpinski/images/AlCell_LR.jpg b/tools/moltemplate/examples/silly/sierpinski/images/AlCell_LR.jpg new file mode 100644 index 0000000000..bf07914dac Binary files /dev/null and b/tools/moltemplate/examples/silly/sierpinski/images/AlCell_LR.jpg differ diff --git a/tools/moltemplate/examples/silly/sierpinski/images/lvl1_LR.jpg b/tools/moltemplate/examples/silly/sierpinski/images/lvl1_LR.jpg new file mode 100644 index 0000000000..11174969a3 Binary files /dev/null and b/tools/moltemplate/examples/silly/sierpinski/images/lvl1_LR.jpg differ diff --git a/tools/moltemplate/examples/silly/sierpinski/images/lvl2_LR.jpg b/tools/moltemplate/examples/silly/sierpinski/images/lvl2_LR.jpg new file mode 100644 index 0000000000..744c9af633 Binary files /dev/null and b/tools/moltemplate/examples/silly/sierpinski/images/lvl2_LR.jpg differ diff --git a/tools/moltemplate/examples/silly/sierpinski/images/lvl3_LR.jpg b/tools/moltemplate/examples/silly/sierpinski/images/lvl3_LR.jpg new file mode 100644 index 0000000000..a72a1ea8d0 Binary files /dev/null and b/tools/moltemplate/examples/silly/sierpinski/images/lvl3_LR.jpg differ diff --git a/tools/moltemplate/examples/silly/sierpinski/images/serpinski_cube_lattice_8cells_t=0_zoom1_LR2.jpg b/tools/moltemplate/examples/silly/sierpinski/images/serpinski_cube_lattice_8cells_t=0_zoom1_LR2.jpg new file mode 100644 index 0000000000..9020a3be0e Binary files /dev/null and b/tools/moltemplate/examples/silly/sierpinski/images/serpinski_cube_lattice_8cells_t=0_zoom1_LR2.jpg differ diff --git a/tools/moltemplate/examples/silly/sierpinski/images/serpinski_cube_lattice_8cells_t=7400_LR.jpg b/tools/moltemplate/examples/silly/sierpinski/images/serpinski_cube_lattice_8cells_t=7400_LR.jpg new file mode 100644 index 0000000000..0036c903a2 Binary files /dev/null and b/tools/moltemplate/examples/silly/sierpinski/images/serpinski_cube_lattice_8cells_t=7400_LR.jpg differ diff --git a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/al_cell.lt b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/al_cell.lt new file mode 100644 index 0000000000..3054a45e01 --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/al_cell.lt @@ -0,0 +1,64 @@ +# "AlCell" defines the 4-atom FCC unit cell +# of Aluminum (with a 4.05 angstrom spacing) + +AlCell { + + # AtomID MolID(IGNORE!) AtomType Charge X Y Z + + write("Data Atoms") { + $atom:AlC $mol:... @atom:Al 0.0 0.000 0.000 0.000 + $atom:AlX $mol:... @atom:Al 0.0 0.000 2.025 2.025 + $atom:AlY $mol:... @atom:Al 0.0 2.025 0.000 2.025 + $atom:AlZ $mol:... @atom:Al 0.0 2.025 2.025 0.000 + } + + write_once("In Init") { + units metal + atom_style full # <- Requires each atom has a MolID and Charge. + # This is not necessary. (Why use "full"? + # The "full" atom style is useful if you want to + # mix the aluminum with other molecules later. + # Otherwise, just use "atom_style atomic", and + # and remove the 2nd and 4th columns above.) + pair_style eam/alloy + } + + write_once("In Settings") { + pair_coeff * * Al99.eam.alloy Al + } + + write_once("Data Masses") { + @atom:Al 27.0 + } + +} # AlCell + + + + + +# Here is an alternate way to define AlCell +# using "scale(4.05)" to select the lattice spacing: +# +#FccCell { +# write("Data Atoms") { +# $atom:AlC $mol:... @atom:Al 0.0 0.0 0.0 0.0 +# $atom:AlX $mol:... @atom:Al 0.0 0.0 0.5 0.5 +# $atom:AlY $mol:... @atom:Al 0.0 0.5 0.0 0.5 +# $atom:AyZ $mol:... @atom:Al 0.0 0.5 0.5 0.0 +# } +# write_once("Data Masses") { +# @atom:Al 27.0 +# } +# write_once("In Init") { +# units metal +# atom_style full +# pair_style eam/alloy +# } +# write_once("In Settings") { +# pair_coeff * * Al99.eam.alloy Al +# } +#} +# +#AlCell = FccCell.scale(4.05) +# diff --git a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/al_cell.lt b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/al_cell.lt new file mode 100644 index 0000000000..3054a45e01 --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/al_cell.lt @@ -0,0 +1,64 @@ +# "AlCell" defines the 4-atom FCC unit cell +# of Aluminum (with a 4.05 angstrom spacing) + +AlCell { + + # AtomID MolID(IGNORE!) AtomType Charge X Y Z + + write("Data Atoms") { + $atom:AlC $mol:... @atom:Al 0.0 0.000 0.000 0.000 + $atom:AlX $mol:... @atom:Al 0.0 0.000 2.025 2.025 + $atom:AlY $mol:... @atom:Al 0.0 2.025 0.000 2.025 + $atom:AlZ $mol:... @atom:Al 0.0 2.025 2.025 0.000 + } + + write_once("In Init") { + units metal + atom_style full # <- Requires each atom has a MolID and Charge. + # This is not necessary. (Why use "full"? + # The "full" atom style is useful if you want to + # mix the aluminum with other molecules later. + # Otherwise, just use "atom_style atomic", and + # and remove the 2nd and 4th columns above.) + pair_style eam/alloy + } + + write_once("In Settings") { + pair_coeff * * Al99.eam.alloy Al + } + + write_once("Data Masses") { + @atom:Al 27.0 + } + +} # AlCell + + + + + +# Here is an alternate way to define AlCell +# using "scale(4.05)" to select the lattice spacing: +# +#FccCell { +# write("Data Atoms") { +# $atom:AlC $mol:... @atom:Al 0.0 0.0 0.0 0.0 +# $atom:AlX $mol:... @atom:Al 0.0 0.0 0.5 0.5 +# $atom:AlY $mol:... @atom:Al 0.0 0.5 0.0 0.5 +# $atom:AyZ $mol:... @atom:Al 0.0 0.5 0.5 0.0 +# } +# write_once("Data Masses") { +# @atom:Al 27.0 +# } +# write_once("In Init") { +# units metal +# atom_style full +# pair_style eam/alloy +# } +# write_once("In Settings") { +# pair_coeff * * Al99.eam.alloy Al +# } +#} +# +#AlCell = FccCell.scale(4.05) +# diff --git a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/sierpinski_cubes.lt b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/sierpinski_cubes.lt new file mode 100644 index 0000000000..28c2d5ea24 --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/sierpinski_cubes.lt @@ -0,0 +1,34 @@ +import "al_cell.lt" # <- defines the 4-atom "AlCell" FCC Aluminum unit cell + +# This approach uses the "delete" command. +# It works and it is elegant, but because the majority of atoms will be +# deleted, (and because memory is allocated for all atoms, including +# deleted atoms) this approach is not very memory efficient. + +SierpinskiCubeLvl1 { + cells = new AlCell [3].move(0.00, 0.00, 4.05) + [3].move(0.00, 4.05, 0.00) + [3].move(4.05, 0.00, 0.00) + delete cells[*][1][1] + delete cells[1][*][1] + delete cells[1][1][*] +} + +SierpinskiCubeLvl2 { + cells = new SierpinskiCubeLvl1 [3].move(0.00, 0.00, 12.15) + [3].move(0.00, 12.15, 0.00) + [3].move(12.15, 0.00, 0.00) + delete cells[*][1][1] + delete cells[1][*][1] + delete cells[1][1][*] +} + +SierpinskiCubeLvl3 { + cells = new SierpinskiCubeLvl2 [3].move(0.00, 0.00, 36.45) + [3].move(0.00, 36.45, 0.00) + [3].move(36.45, 0.00, 0.00) + delete cells[*][1][1] + delete cells[1][*][1] + delete cells[1][1][*] +} + diff --git a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/system.lt b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/system.lt new file mode 100644 index 0000000000..b14929e986 --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/system.lt @@ -0,0 +1,34 @@ +# Periodic boundary conditions: +write_once("Data Boundary") { + 0.0 72.9 xlo xhi + 0.0 72.9 ylo yhi + 0.0 72.9 zlo zhi +} + +import "sierpinski_cubes.lt" + +cells = new SierpinskiCubeLvl2 [2].move(0.00, 0.00, 36.45) + [2].move(0.00, 36.45, 0.00) + [2].move(36.45, 0.00, 0.00) +delete cells[*][1][1] +delete cells[1][*][1] +delete cells[1][1][*] + + + + + + + + + + + + +################################################################ +# The next command is not necessary: +# + create_var { $mol } # <-This forces all of the Al atoms in the crystal +# # to share the same molecule ID number. +# # Molecule ID numbers are not necessary. Ignore this. +# diff --git a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/sierpinski_cubes.lt b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/sierpinski_cubes.lt new file mode 100644 index 0000000000..d45a8331b1 --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/sierpinski_cubes.lt @@ -0,0 +1,66 @@ +import "al_cell.lt" # <- defines the 4-atom "AlCell" FCC Aluminum unit cell + +# A Sierpinski cube resembles a 3x3x3 Rubik's-cube-like object with the smaller +# cube in each central face (and in the interior) removed. There are 3x3x3-7=20 +# remaining sub-cubes. Each of these 20 sub-cubes is a smaller SierpinskiCube. +# To build a SierpinskiCube, you can list all 20 sub-cubes, or you can fill a +# 3x3x3 cube with sub-cubes and delete the interior sub-cubes. (The later +# approach is used in file "elegant_inefficient_version/sierpinski_cubes.lt") + + + +SierpinskiCubeLvl1 { + # Again, a Sierpinski-cube is constructed of 20 smaller cube-shaped objects. + # Here, the small cube-shaped objects are "AlCells" (defined in "al_cell.lt"). + # I could list out the positions of all 20 AlCells, (and this would be clearer + # for the reader). However instead I built it from a combination of + # two-dimensional and three-dimensional arrays of AlCells (explained below). + + # The next command creates 4 AlCells at: (0, 4.05, 0.0), (8.1, 4.05, 0.0), + # (0, 4.05, 8.1), (8.1, 4.05, 8.1) + + cells_xz = new AlCell.move(0.00, 4.05, 0.00) [2].move(8.10, 0.0, 0.0 ) + [2].move(0.0, 0.0, 8.10) + + # The next command creates 4 AlCells at: (4.05, 0, 0.0), (4.05, 8.1, 0.0), + # (4.05, 0, 8.1), (4.05, 8.1, 8.1) + + cells_yz = new AlCell.move(4.05, 0.00, 0.00) [2].move(0.0, 8.10, 0.0 ) + [2].move(0.0, 0.0, 8.10) + + # The next command creates 12 AlCells (2x2x3) at: + # (0.0, 0.0, 0.0), (0.0, 0.0, 4.05), (0.0, 0.0, 8.1) + # (0.0, 8.1, 0.0), (0.0, 8.1, 4.05), (0.0, 8.1, 8.1) + # (8.1, 8.1, 0.0), (8.1, 8.1, 4.05), (8.1, 8.1, 8.1) + + cells_z = new AlCell [2].move(8.10, 0.00, 0.00) + [2].move(0.00, 8.10, 0.00) + [3].move(0.00, 0.00, 4.05) +} + + + +SierpinskiCubeLvl2 { + # Identical arrangement to SierpinskiCube1 (with 3x larger length scales) + cells_xz= new SierpinskiCubeLvl1.move(0.0,12.15,0.0) [2].move(24.3, 0.0, 0.0 ) + [2].move(0.0, 0.0, 24.3) + cells_yz= new SierpinskiCubeLvl1.move(12.15,0.0,0.0) [2].move(0.0, 24.3, 0.0 ) + [2].move(0.0, 0.0, 24.3) + cells_z = new SierpinskiCubeLvl1 [2].move(24.3, 0.00, 0.00) + [2].move(0.00, 24.3, 0.00) + [3].move(0.00, 0.00, 12.15) +} + + + +SierpinskiCubeLvl3 { + # Identical arrangement to SierpinskiCube2 (with 3x larger length scales) + cells_xz= new SierpinskiCubeLvl2.move(0.0,36.45,0.0) [2].move(72.9, 0.0, 0.0 ) + [2].move(0.0, 0.0, 72.9) + cells_yz= new SierpinskiCubeLvl2.move(36.45,0.0,0.0) [2].move(0.0, 72.9, 0.0 ) + [2].move(0.0, 0.0, 72.9) + cells_z = new SierpinskiCubeLvl2 [2].move(72.9, 0.00, 0.00) + [2].move(0.00, 72.9, 0.00) + [3].move(0.00, 0.00, 36.45) +} + diff --git a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/system.lt b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/system.lt new file mode 100644 index 0000000000..b226b77eed --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/system.lt @@ -0,0 +1,36 @@ +# Periodic boundary conditions: +write_once("Data Boundary") { + 0.0 218.7 xlo xhi + 0.0 218.7 ylo yhi + 0.0 218.7 zlo zhi +} + +import "sierpinski_cubes.lt" + +cells_xyz = new SierpinskiCubeLvl3.move(0.0000, 0.0000, 0.0000) +cells_Xyz = new SierpinskiCubeLvl3.move(109.35, 0.0000, 0.0000) +cells_xYz = new SierpinskiCubeLvl3.move(0.0000, 109.35, 0.0000) +cells_xyZ = new SierpinskiCubeLvl3.move(0.0000, 0.0000, 109.35) + + + + + + + + + + + + + + + + +################################################################ +# The next command is not necessary: +# + create_var { $mol } # <-This forces all of the Al atoms in the crystal +# # to share the same molecule ID number. +# # Molecule ID numbers are not necessary. Ignore this. +# diff --git a/tools/moltemplate/examples/silly/sierpinski/run.in b/tools/moltemplate/examples/silly/sierpinski/run.in new file mode 100644 index 0000000000..6b9ad17e6e --- /dev/null +++ b/tools/moltemplate/examples/silly/sierpinski/run.in @@ -0,0 +1,38 @@ +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings + +# ------------------------------- Run Section ------------------------------- +# +# Some of the run-settings below were stolen from: +# +# http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression + +# EQUILIBRATION +reset_timestep 0 +timestep 0.001 +velocity all create 300 12345 mom yes rot no +fix 1 all npt temp 300 300 1 iso 0 0 1 drag 1 + +# Output files +thermo 100 +thermo_style custom step ke pe press +dump dCoords all custom 100 traj.lammpstrj id type x y z ix iy iz + +run 20000 + +# Run for at least 10 picosecond (assuming 1 fs timestep) +run 10000 + + +###################################### +# SIMULATION DONE +print "All done" diff --git a/tools/moltemplate/moltemplate_manual.pdf b/tools/moltemplate/moltemplate_manual.pdf new file mode 100644 index 0000000000..c13842d230 Binary files /dev/null and b/tools/moltemplate/moltemplate_manual.pdf differ diff --git a/tools/moltemplate/src/extract_lammps_data.py b/tools/moltemplate/src/extract_lammps_data.py new file mode 100755 index 0000000000..4fe3ec743d --- /dev/null +++ b/tools/moltemplate/src/extract_lammps_data.py @@ -0,0 +1,119 @@ +#!/usr/bin/env python + +lammps_data_sections = set(['Atoms', + 'Masses', + 'Bonds', + 'Bond Coeffs', + 'Angles', + 'Angle Coeffs', + 'Dihedrals', + 'Dihedral Coeffs', + 'Impropers', + 'Improper Coeffs', + 'BondBond Coeffs', # class2 angles + 'BondAngle Coeffs', # class2 angles + 'MiddleBondTorsion Coeffs', # class2 dihedrals + 'EndBondTorsion Coeffs', # class2 dihedrals + 'AngleTorsion Coeffs', # class2 dihedrals + 'AngleAngleTorsion Coeffs', # class2 dihedrals + 'BondBond13 Coeffs', # class2 dihedrals + 'AngleAngle Coeffs', # class2 impropers + 'Angles By Type', # new. not standard LAMMPS + 'Dihedrals By Type',# new. not standard LAMMPS + 'Angles By Type']) # new. not standard LAMMPS + + +def DeleteComments(string, + escape='\\', + comment_char='#'): + escaped_state = False + for i in range(0,len(string)): + if string[i] in escape: + if escaped_state: + escaped_state = False + else: + escaped_state = True + elif string[i] == comment_char: + if not escaped_state: + return string[0:i] + return string + + + +def ExtractDataSection(f, + section_name, + comment_char = '#', + include_section_name = False, + return_line_nums = False): + + inside_section = False + if section_name in ('header','Header'): #"Header" section includes beginning + inside_section = True + + nonblank_encountered = False + nonheader_encountered = False + + i = 0 + for line_orig in f: + return_this_line = False + line = DeleteComments(line_orig).strip() + if line in lammps_data_sections: + nonheader_encountered = True + if section_name in ('header', 'Header'): + # The "header" section includes all lines at the beginning of the + # before any other section is encountered. + if nonheader_encountered: + return_this_line = False + else: + return_this_line = True + elif line == section_name: + inside_section = True + nonblank_encountered = False + if include_section_name: + return_this_line = True + # A block of blank lines (which dont immediately follow + # the section_name) signal the end of a section: + elif len(line) == 0: + if inside_section and include_section_name: + return_this_line = True + if nonblank_encountered: + inside_section = False + elif line[0] != comment_char: + if inside_section: + nonblank_encountered = True + return_this_line = True + + if return_this_line: + if return_line_nums: + yield i + else: + yield line_orig + + i += 1 + + + +if __name__ == "__main__": + + import sys + lines = sys.stdin.readlines() + exclude_sections = False + if sys.argv[1] == '-n': + exclude_sections = True + del sys.argv[1] + + if not exclude_sections: + for section_name in sys.argv[1:]: + for line in ExtractDataSection(lines, section_name): + sys.stdout.write(line) + else: + line_nums_exclude = set([]) + for section_name in sys.argv[1:]: + for line_num in ExtractDataSection(lines, + section_name, + include_section_name=True, + return_line_nums=True): + line_nums_exclude.add(line_num) + for i in range(0, len(lines)): + if i not in line_nums_exclude: + sys.stdout.write(lines[i]) diff --git a/tools/moltemplate/src/ltemplify.py b/tools/moltemplate/src/ltemplify.py new file mode 100755 index 0000000000..000d0692a7 --- /dev/null +++ b/tools/moltemplate/src/ltemplify.py @@ -0,0 +1,2034 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +# Author: Andrew Jewett (jewett.aij at g mail) +# http://www.chem.ucsb.edu/~sheagroup +# License: 3-clause BSD License (See LICENSE.TXT) +# Copyright (c) 2012, Regents of the University of California +# All rights reserved. + +""" +ltemplify.py + +The "ltemplify.py" script can be used to convert existing LAMMPS +input script and data files into a single .ttree file +(which includes both topology and force-field information + for a single molecule in your system). + +Example: + + ltemplify.py -name Mol file.in file.data > mol.ttree + +This creates a template for a new type of molecule (named "Mol"), +consisting of all the atoms in the lammps files you included, +and saves this data in a single ttree file ("mol.ttree"). +This file can be used with moltemplate/ttree to +define large systems containing this molecule. + +""" + +import sys +from ttree_lex import * +from lttree_styles import * + + + +def Intify(s): + if s.isdigit(): + return int(s) + elif s[0:2] == 'id': + return int(s[2:]) + elif s[0:4] == 'type': + return int(s[4:]) + else: + return s + +def StringToInterval(sel_str, slice_delim='*'): + i_slice = sel_str.find(slice_delim) + + if i_slice == -1: + if sel_str.isdigit(): + a = int(sel_str) + b = int(sel_str) + else: + a = sel_str + b = sel_str + + else: + a = sel_str[:i_slice] + b = sel_str[i_slice+len(slice_delim):] + + if (((len(a)>0) and (not a.isdigit())) or + ((len(b)>0) and (not b.isdigit()))): + raise InputError('Error: invalid selection string \"'+ + sel_str+'\"\n') + if (len(a) > 0): + a = int(a) + else: + a = None + + if (len(b) > 0): + b = int(b) + else: + b = None + + return a,b + + +# Selections are simply lists of 2-tuples (pairs) + +def LammpsSelectToIntervals(sel_str, slice_delim='*', or_delim=', '): + + """ + This function converts a string such as "1*4 6 9*12" into + a list of tuples, for example: [(1,4), (6,6), (9,12)] + In general, the of intervals has the form: + [(a1,b1), (a2,b2), (a3,b3), ... ] + + An atom is considered to belong to this selection + if it happens to lie within the closed interval [a,b] + for any pair of a,b values in the list of intervals. + If for a given pair a,b, either a or b is "None", then that a or b + value is not used to disqualify membership in the interval. + (Similar to -infinity or +infinity. In other words if a is set to None, + then to belong to the interval it is enough to be less than b.) + + """ + selection_list = [] + #tokens = sel_str.split(or_delim) <-- Not what we want when len(or_delim)>1 + tokens = LineLex.TextBlock2Lines(sel_str, or_delim, keep_delim=False) + for token in tokens: + token = token.strip() + (a,b) = StringToInterval(token, slice_delim) + selection_list.append((a, b)) + + return selection_list + + +def IntervalListToMinMax(interval_list): + min_a = None + max_b = None + for (a,b) in interval_list: + if ((not (type(a) is int)) or (not (type(b) is int))): + return None,None #only integer min/max makes sense. otherwise skip + + if (min_a == None) or (a < min_a): + min_a = a + if (max_b == None) or (b > max_b): + max_b = b + return min_a, max_b + + +def BelongsToSel(i, sel): + if (i == None) or (sel == None) or (len(sel) == 0): + # If the user has not specified a selection for this category, + # then by default all objects are accepted + return True + + elif (type(i) is str): + if i.isdigit(): + i = int(i) + else: + return True + + belongs = False + for interval in sel: + assert(len(interval) == 2) + if interval[0]: + if i >= interval[0]: + if (interval[1] == None) or (i <= interval[1]): + belongs = True + break + elif interval[1]: + if i <= interval[1]: + belongs = True + break + else: + # In that case, the user entered something like "*" + # which covers all possible numbers + belongs = True + break + + return belongs + + + +try: + + g_program_name = __file__.split('/')[-1] # = 'lemplify.py' + g_version_str = '0.3' + g_date_str = '2012-12-11' + sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+'\n') + + non_empty_output = False + no_warnings = True + indent = 2 + cindent = 0 + atomid_selection = [] + atomtype_selection = [] + molid_selection = [] + mol_name = '' + + min_sel_atomid = None + min_sel_atomtype = None + min_sel_bondid = None + min_sel_bondtype = None + min_sel_angleid = None + min_sel_angletype = None + min_sel_dihedralid = None + min_sel_dihedraltype = None + min_sel_improperid = None + min_sel_impropertype = None + + max_sel_atomid = None + max_sel_atomtype = None + max_sel_bondid = None + max_sel_bondtype = None + max_sel_angleid = None + max_sel_angletype = None + max_sel_dihedralid = None + max_sel_dihedraltype = None + max_sel_improperid = None + max_sel_impropertype = None + + needed_atomids = set([]) + needed_atomtypes = set([]) + needed_bondids = set([]) + needed_bondtypes = set([]) + needed_angleids = set([]) + needed_angletypes = set([]) + needed_dihedralids = set([]) + needed_dihedraltypes = set([]) + needed_improperids = set([]) + needed_impropertypes = set([]) + + min_needed_atomtype = None + max_needed_atomtype = None + min_needed_bondtype = None + max_needed_bondtype = None + min_needed_angletype = None + max_needed_angletype = None + min_needed_dihedraltype = None + max_needed_dihedraltype = None + + + # To process the selections, we need to know the atom style: + atom_style_undefined = True + + i_atomid = None + i_atomtype = None + i_molid = None + + l_in_init = [] + l_in_settings = [] + l_in_masses = [] + l_in_pair_coeffs = [] + l_in_bond_coeffs = [] + l_in_angle_coeffs = [] + l_in_dihedral_coeffs = [] + l_in_improper_coeffs = [] + l_data_masses = [] + l_data_bond_coeffs = [] + l_data_angle_coeffs = [] + l_data_dihedral_coeffs = [] + l_data_improper_coeffs = [] + l_data_pair_coeffs = [] + l_data_atoms = [] + l_data_velocities = [] + l_data_bonds = [] + l_data_angles = [] + l_data_dihedrals = [] + l_data_impropers = [] + + # class2 force fields + l_data_bondbond_coeffs = [] + l_data_bondangle_coeffs = [] + l_data_middlebondtorsion_coeffs = [] + l_data_endbondtorsion_coeffs = [] + l_data_angletorsion_coeffs = [] + l_data_angleangletorsion_coeffs = [] + l_data_bondbond13_coeffs = [] + l_data_angleangle_coeffs = [] + + # non-point-like particles: + l_data_ellipsoids = [] + l_data_lines = [] + l_data_triangles = [] + + # automatic generation of bonded interactions by type: + l_data_angles_by_type = [] + l_data_dihedrals_by_type = [] + l_data_impropers_by_type = [] + + atoms_already_read = False + some_pair_coeffs_read = False + complained_atom_style_mismatch = False + + + argv = sys.argv + + i = 1 + + while i < len(argv): + + #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n') + + if argv[i] == '-columns': + if i+1 >= len(argv): + raise InputError('Error: the \"'+argv[i]+'\" argument should be followed by a quoted\n' + ' string which contains a space-delimited list of the names of\n' + ' of columns in the \"Atoms\" section of the LAMMPS data file.\n' + ' If the list contains the symbols:\n' + ' \"atom-ID\" or \"atomid\", they are interpreted\n' + ' as unique atom ID numbers, and columns named\n' + ' \"atom-type\" or \"atomtype\" are interpreted\n' + ' as atom types. Finally, columns named\n' + ' \"molecule-ID\", \"molecule\", or \"mol-ID\", or \"mol\"\n' + ' are interpreted as unique molecule id numbers.\n' + 'Example:\n' + ' '+argv[i]+' \'atom-ID atom-type q polarizability molecule-ID x y z\'\n' + ' defines a custom atom_style containing the properties\n' + ' atom-ID atom-type q polarizability molecule-ID x y z\n' + ' Make sure you enclose the entire list in quotes.\n'); + column_names = argv[i+1].strip('\"\'').strip().split() + del(argv[i:i+2]) + + elif ((argv[i] == '-name') or + (argv[i] == '-molname') or + (argv[i] == '-molecule-name') or + (argv[i] == '-molecule_name')): + if i+1 >= len(argv): + raise InputError('Error: '+argv[i]+' flag should be followed by a a molecule type name.\n') + cindent = 2 + indent += cindent + mol_name = argv[i+1] + del(argv[i:i+2]) + + elif ((argv[i].lower() == '-atomstyle') or + (argv[i].lower() == '-atom_style') or + (argv[i].lower() == '-atom-style')): + if i+1 >= len(argv): + raise InputError('Error: '+argv[i]+' flag should be followed by a an atom_style name.\n' + ' (or single quoted string which includes a space-separated\n' + ' list of column names).\n') + atom_style_undefined = False + column_names = AtomStyle2ColNames(argv[i+1]) + if (argv[i+1].strip().split()[0] in g_style_map): + l_in_init.append((' '*indent) + 'atom_style ' + argv[i+1] + '\n') + sys.stderr.write('\n \"Atoms\" column format:\n') + sys.stderr.write(' '+(' '.join(column_names))+'\n') + i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names) + if i_molid: + sys.stderr.write(' (i_atomid='+str(i_atomid+1)+', i_atomtype='+str(i_atomtype+1)+', i_molid='+str(i_molid+1)+')\n\n') + else: + sys.stderr.write(' (i_atomid='+str(i_atomid+1)+', i_atomtype='+str(i_atomtype+1)+')\n') + del(argv[i:i+2]) + + elif ((argv[i].lower() == '-id') or + #(argv[i].lower() == '-a') or + #(argv[i].lower() == '-atoms') or + (argv[i].lower() == '-atomid') or + #(argv[i].lower() == '-atomids') or + (argv[i].lower() == '-atom-id') + #(argv[i].lower() == '-atom-ids') or + #(argv[i].lower() == '-$atom') or + #(argv[i].lower() == '-$atoms') + ): + if i+1 >= len(argv): + raise InputError('Error: '+argv[i]+' flag should be followed by a list of integers\n' + ' (or strings). These identify the group of atoms you want to\n' + ' to include in the template you are creating.\n') + atomid_selection += LammpsSelectToIntervals(argv[i+1]) + min_sel_atomid, max_sel_atomid = IntervalListToMinMax(atomid_selection) + del(argv[i:i+2]) + elif ((argv[i].lower() == '-type') or + #(argv[i].lower() == '-t') or + (argv[i].lower() == '-atomtype') or + (argv[i].lower() == '-atom-type') + #(argv[i].lower() == '-atomtypes') or + #(argv[i].lower() == '-atom-types') or + #(argv[i].lower() == '-@atom') or + #(argv[i].lower() == '-@atoms') or + #(argv[i].lower() == '-@atomtype') or + #(argv[i].lower() == '-@atomtypes') + ): + if i+1 >= len(argv): + raise InputError('Error: '+argv[i]+' flag should be followed by a list of integers.\n' + ' (or strings). These identify the group of atom types you want to\n' + ' to include in the template you are creating.\n') + atomtype_selection += LammpsSelectToIntervals(argv[i+1]) + min_sel_atomtype, max_sel_atomtype = IntervalListToMinMax(atomtype_selection) + del(argv[i:i+2]) + elif ((argv[i].lower() == '-mol') or + #(argv[i].lower() == '-m') or + (argv[i].lower() == '-molid') or + #(argv[i].lower() == '-molids') or + (argv[i].lower() == '-mol-id') or + #(argv[i].lower() == '-mol-ids') or + #(argv[i].lower() == '-molecule') or + (argv[i].lower() == '-moleculeid') or + (argv[i].lower() == '-molecule-id') + #(argv[i].lower() == '-molecules') or + #(argv[i].lower() == '-molecule-ids') or + #(argv[i].lower() == '-$mol') or + #(argv[i].lower() == '-$molecule') + ): + if i+1 >= len(argv): + sys.stderr.write('Error: '+argv[i]+' flag should be followed by a list of integers.\n' + ' (or strings). These identify the group of molecules you want to\n' + ' include in the template you are creating.\n') + molid_selection += LammpsSelectToIntervals(argv[i+1]) + del(argv[i:i+2]) + else: + i += 1 + + if atom_style_undefined: + # The default atom_style is "full" + column_names = AtomStyle2ColNames('full') + i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names) + + #--------------------------------------------------------- + #-- The remaining arguments are files that the user wants + #-- us to read and convert. It is typical to have + #-- multiple input files, because LAMMPS users often + #-- store their force field parameters in either the LAMMPS + #-- data files and input script files, or both. + #-- We want to search all of the LAMMPS input files in + #-- order to make sure we extracted all the force field + #-- parameters (coeff commands). + #--------------------------------------------------------- + + for i_arg in range(1,len(argv)): + fname = argv[i_arg] + try: + lammps_file = open(fname, 'r') + except IOError: + raise InputError('Error: unrecognized argument (\"'+fname+'\"),\n' + ' OR unable to open file:\n' + '\n' + ' \"'+fname+'\"\n' + ' for reading.\n' + '\n' + ' (If you were not trying to open a file with this name,\n' + ' then there is a problem in your argument list.)\n') + + sys.stderr.write('reading file \"'+fname+'\"\n') + + atomid2type = {} + atomid2mol = {} + data_file_header_names = set(['LAMMPS Description', + 'Atoms', 'Masses', 'Velocities', 'Bonds', + 'Angles', 'Dihedrals', 'Impropers', + 'Pair Coeffs', + 'Bond Coeffs', 'Angle Coeffs', + 'Dihedral Coeffs', 'Improper Coeffs', + #class2 force fields: + 'BondBond Coeffs', 'BondAngle Coeffs', + 'MiddleBondTorsion Coeffs', 'EndBondTorsion Coeffs', + 'AngleTorsion Coeffs', 'AngleAngleTorsion Coeffs', + 'BondBond13 Coeffs', + 'AngleAngle Coeffs', + # non-point-like particles: + 'Ellipsoids', 'Triangles', 'Lines', + #specifying bonded interactions by type: + 'Angles By Type', 'Dihedrals By Type', 'Impropers By Type' + ]) + + lex=LineLex(lammps_file, fname) + lex.source_triggers = set(['include','import']) + # set up lex to accept most characters in file names: + lex.wordterminators = '(){}' + lex.whitespace + # set up lex to understand the "include" statement: + lex.source = 'include' + lex.escape = '\\' + + while lex: + infile = lex.infile + lineno = lex.lineno + line = lex.ReadLine() + if (lex.infile != infile): + infile = lex.infile + lineno = lex.lineno + + #sys.stderr.write(' processing \"'+line.strip()+'\", (\"'+infile+'\":'+str(lineno)+')\n') + + if line == '': + break + + tokens = line.strip().split() + if (len(tokens) > 0): + if ((tokens[0] == 'atom_style') and + atom_style_undefined): + + sys.stderr.write(' Atom Style found. Processing: \"'+line.strip()+'\"\n') + if atoms_already_read: + raise InputError('Error: The file containing the \"atom_style\" command must\n' + ' come before the data file in the argument list.\n' + ' (The templify program needs to know the atom style before reading\n' + ' the data file. Either change the order of arguments so that the\n' + ' LAMMPS input script file is processed before the data file, or use\n' + ' the \"-atom_style\" command line argument to specify the atom_style.)\n') + + column_names = AtomStyle2ColNames(line.split()[1]) + i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names) + + sys.stderr.write('\n \"Atoms\" column format:\n') + sys.stderr.write(' '+(' '.join(column_names))+'\n') + if i_molid: + sys.stderr.write(' (i_atomid='+str(i_atomid+1)+', i_atomtype='+str(i_atomtype+1)+', i_molid='+str(i_molid+1)+')\n\n') + else: + sys.stderr.write(' (i_atomid='+str(i_atomid+1)+', i_atomtype='+str(i_atomtype+1)+')\n\n') + l_in_init.append((' '*indent)+line.lstrip()) + + elif (tokens[0] in set(['units', + 'angle_style', + 'bond_style', + 'dihedral_style', + 'impoper_style', + 'min_style', + 'pair_style', + 'pair_modify', + 'special_bonds', + 'kspace_style', + 'kspace_modify'])): + l_in_init.append((' '*indent)+line.lstrip()) + + #if (line.strip() == 'LAMMPS Description'): + # sys.stderr.write(' processing \"'+line.strip()+'\"\n') + # # skip over this section + # while lex: + # line = lex.ReadLine() + # if line.strip() in data_file_header_names: + # lex.push_raw_text(line) # <- Save line for later + # break + + elif (line.strip() == 'Atoms'): + sys.stderr.write(' processing \"'+line.strip()+'\"\n') + atoms_already_read = True + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + if ((len(tokens) <= i_atomid) or + (len(tokens) <= i_atomtype) or + ((i_molid != None) and + (len(tokens) <= i_molid))): + raise InputError('Error: The number of columns in the \"Atoms\" section does\n' + ' not match the atom_style (see column name list above).\n') + elif ((len(tokens) != len(column_names)) and + (not complained_atom_style_mismatch)): + complained_atom_style_mismatch = True + sys.stderr.write('Warning: The number of columns in the \"Atoms\" section does\n' + ' not match the atom_style (see column name list above).\n') + # this is not a very serious warning. + #no_warnings = False <--no need. commenting out + + + atomid = Intify(tokens[i_atomid]) + atomtype = Intify(tokens[i_atomtype]) + + molid = None + if i_molid: + molid = Intify(tokens[i_molid]) + + atomid2type[atomid] = atomtype + if i_molid: + atomid2mol[atomid] = molid + + + if (BelongsToSel(atomid, atomid_selection) and + BelongsToSel(atomtype, atomtype_selection) and + BelongsToSel(molid, molid_selection)): + tokens[i_atomid] = '$atom:id'+tokens[i_atomid] + tokens[i_atomtype] = '@atom:type'+tokens[i_atomtype] + if i_molid: + tokens[i_molid] = '$mol:id'+tokens[i_molid] + l_data_atoms.append((' '*indent)+(' '.join(tokens)+'\n')) + needed_atomids.add(atomid) + needed_atomtypes.add(int(atomtype)) + + for atomtype in needed_atomtypes: + if type(atomtype) is int: + if ((min_needed_atomtype == None) or + (min_needed_atomtype > atomtype)): + min_needed_atomtype = atomtype + if ((max_needed_atomtype == None) or + (max_needed_atomtype < atomtype)): + max_needed_atomtype = atomtype + + + elif (line.strip() == 'Masses'): + sys.stderr.write(' processing \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + atomtype = Intify(tokens[0]) + if BelongsToSel(atomtype, atomtype_selection): + #tokens[0] = '@atom:type'+tokens[0] + l_data_masses.append((' '*indent)+(' '.join(tokens)+'\n')) + elif (line.strip() == 'Velocities'): + sys.stderr.write(' processing \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + atomid = Intify(tokens[0]) + atomtype = None + if atomid in atomid2type: + atomtype = atomid2type[atomid] + moldid = None + if atomid in atomid2mol: + molid = atomid2mol[atomid] + if (BelongsToSel(atomid, atomid_selection) and + BelongsToSel(atomtype, atomtype_selection) and + BelongsToSel(molid, molid_selection)): + tokens[0] = '$atom:id'+tokens[0] + l_data_velocities.append((' '*indent)+(' '.join(tokens)+'\n')) + + # non-point-like-particles: + elif (line.strip() == 'Ellipsoids'): + sys.stderr.write(' processing \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + atomid = Intify(tokens[0]) + atomtype = None + if atomid in atomid2type: + atomtype = atomid2type[atomid] + moldid = None + if atomid in atomid2mol: + molid = atomid2mol[atomid] + if (BelongsToSel(atomid, atomid_selection) and + BelongsToSel(atomtype, atomtype_selection) and + BelongsToSel(molid, molid_selection)): + tokens[0] = '$atom:id'+tokens[0] + l_data_ellipsoids.append((' '*indent)+(' '.join(tokens)+'\n')) + elif (line.strip() == 'Lines'): + sys.stderr.write(' processing \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + atomid = Intify(tokens[0]) + atomtype = None + if atomid in atomid2type: + atomtype = atomid2type[atomid] + moldid = None + if atomid in atomid2mol: + molid = atomid2mol[atomid] + if (BelongsToSel(atomid, atomid_selection) and + BelongsToSel(atomtype, atomtype_selection) and + BelongsToSel(molid, molid_selection)): + tokens[0] = '$atom:id'+tokens[0] + l_data_lines.append((' '*indent)+(' '.join(tokens)+'\n')) + elif (line.strip() == 'Triangles'): + sys.stderr.write(' processing \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + atomid = Intify(tokens[0]) + atomtype = None + if atomid in atomid2type: + atomtype = atomid2type[atomid] + moldid = None + if atomid in atomid2mol: + molid = atomid2mol[atomid] + if (BelongsToSel(atomid, atomid_selection) and + BelongsToSel(atomtype, atomtype_selection) and + BelongsToSel(molid, molid_selection)): + tokens[0] = '$atom:id'+tokens[0] + l_data_triangles.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'Bonds'): + sys.stderr.write(' processing \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + if (len(tokens) < 4): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical line in Bonds section:\n' + ' \"'+line.strip()+'\"\n') + #tokens[0] = '$bond:id'+tokens[0] + #tokens[1] = '@bond:type'+tokens[1] + atomids = [None, None] + atomtypes = [None, None] + molids = [None, None] + in_selections = True + some_in_selection = False + for n in range(0,2): + atomids[n] = Intify(tokens[2+n]) + if atomids[n] in atomid2type: + atomtypes[n] = atomid2type[atomids[n]] + if atomids[n] in atomid2mol: + molids[n] = atomid2mol[atomids[n]] + if (BelongsToSel(atomids[n], atomid_selection) and + BelongsToSel(atomtypes[n], atomtype_selection) and + BelongsToSel(molids[n], molid_selection)): + #tokens[2+n] = '$atom:id'+tokens[2+n] + some_in_selection = True + else: + in_selections = False + if in_selections: + l_data_bonds.append((' '*indent)+(' '.join(tokens)+'\n')) + elif some_in_selection: + sys.stderr.write('WARNING: SELECTION BREAKS BONDS\n') + sys.stderr.write(' (between atom ids: ') + + for n in range(0,2): + sys.stderr.write(str(atomids[n])+' ') + sys.stderr.write(')\n' + ' The atoms you selected are bonded\n' + ' to other atoms you didn\'t select.\n' + ' Are you sure you selected the correct atoms?\n') + no_warnings = False + + + + elif (line.strip() == 'Angles'): + sys.stderr.write(' processing \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line == '': + break + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + if (len(tokens) < 5): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical line in Angles section:\n' + ' \"'+line.strip()+'\"\n') + #tokens[0] = '$angle:id'+tokens[0] + #tokens[1] = '@angle:type'+tokens[1] + atomids = [None, None, None] + atomtypes = [None, None, None] + molids = [None, None, None] + in_selections = True + some_in_selection = False + for n in range(0,3): + atomids[n] = Intify(tokens[2+n]) + if atomids[n] in atomid2type: + atomtypes[n] = atomid2type[atomids[n]] + if atomids[n] in atomid2mol: + molids[n] = atomid2mol[atomids[n]] + if (BelongsToSel(atomids[n], atomid_selection) and + BelongsToSel(atomtypes[n], atomtype_selection) and + BelongsToSel(molids[n], molid_selection)): + #tokens[2+n] = '$atom:id'+tokens[2+n] + some_in_selection = True + else: + in_selections = False + if in_selections: + l_data_angles.append((' '*indent)+(' '.join(tokens)+'\n')) + elif some_in_selection: + sys.stderr.write('WARNING: SELECTION BREAKS ANGLES\n') + sys.stderr.write(' (between atom ids: ') + for n in range(0,3): + sys.stderr.write(str(atomids[n])+' ') + sys.stderr.write(')\n' + ' The atoms you selected participate in 3-body \"Angle\"\n' + ' interactions with other atoms you didn\'t select.\n' + ' (They will be ignored.)\n' + ' Are you sure you selected the correct atoms?\n') + no_warnings = False + + + elif (line.strip() == 'Dihedrals'): + sys.stderr.write(' processing \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + if (len(tokens) < 6): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical line in Dihedrals section:\n' + ' \"'+line.strip()+'\"\n') + #tokens[0] = '$dihedral:id'+tokens[0] + #tokens[1] = '@dihedral:type'+tokens[1] + atomids = [None, None, None, None] + atomtypes = [None, None, None, None] + molids = [None, None, None, None] + in_selections = True + some_in_selection = False + for n in range(0,4): + atomids[n] = Intify(tokens[2+n]) + if atomids[n] in atomid2type: + atomtypes[n] = atomid2type[atomids[n]] + if atomids[n] in atomid2mol: + molids[n] = atomid2mol[atomids[n]] + if (BelongsToSel(atomids[n], atomid_selection) and + BelongsToSel(atomtypes[n], atomtype_selection) and + BelongsToSel(molids[n], molid_selection)): + #tokens[2+n] = '$atom:id'+tokens[2+n] + some_in_selection = True + else: + in_selections = False + if in_selections: + l_data_dihedrals.append((' '*indent)+(' '.join(tokens)+'\n')) + elif some_in_selection: + sys.stderr.write('WARNING: SELECTION BREAKS DIHEDRALS\n') + sys.stderr.write(' (between atom ids: ') + for n in range(0,4): + sys.stderr.write(str(atomids[n])+' ') + sys.stderr.write(')\n' + ' The atoms you selected participate in 4-body \"Dihedral\"\n' + ' interactions with other atoms you didn\'t select.\n' + ' (They will be ignored.)\n' + ' Are you sure you selected the correct atoms?\n') + no_warnings = False + + + elif (line.strip() == 'Impropers'): + sys.stderr.write(' processing \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + if (len(tokens) < 6): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical line in Impropers section:\n' + ' \"'+line.strip()+'\"\n') + #tokens[0] = '$improper:id'+tokens[0] + #tokens[1] = '@improper:type'+tokens[1] + atomids = [None, None, None, None] + atomtypes = [None, None, None, None] + molids = [None, None, None, None] + in_selections = True + some_in_selection = False + for n in range(0,4): + atomids[n] = Intify(tokens[2+n]) + if atomids[n] in atomid2type: + atomtypes[n] = atomid2type[atomids[n]] + if atomids[n] in atomid2mol: + molids[n] = atomid2mol[atomids[n]] + if (BelongsToSel(atomids[n], atomid_selection) and + BelongsToSel(atomtypes[n], atomtype_selection) and + BelongsToSel(molids[n], molid_selection)): + #tokens[2+n] = '$atom:id'+tokens[2+n] + some_in_selection = True + else: + in_selections = False + if in_selections: + l_data_impropers.append((' '*indent)+(' '.join(tokens)+'\n')) + elif some_in_selection: + sys.stderr.write('WARNING: SELECTION BREAKS IMPROPERS\n') + sys.stderr.write(' (between atom ids: ') + for n in range(0,4): + sys.stderr.write(str(atomids[n])+' ') + sys.stderr.write(')\n' + ' The atoms you selected participate in 4-body \"Improper\"\n' + ' interactions with other atoms you didn\'t select.\n' + ' (They will be ignored.)\n' + ' Are you sure you selected the correct atoms?\n') + no_warnings = False + + + elif (line.strip() == 'Bond Coeffs'): + sys.stderr.write(' processing \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + #tokens[0] = '@bond:type'+tokens[0] + l_data_bond_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'Angle Coeffs'): + sys.stderr.write(' processing \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + #tokens[0] = '@angle:type'+tokens[0] + l_data_angle_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'Dihedral Coeffs'): + sys.stderr.write(' processing \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + #tokens[0] = '@dihedral:type'+tokens[0] + l_data_dihedral_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'Improper Coeffs'): + sys.stderr.write(' processing \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + #tokens[0] = '@improper:type'+tokens[0] + l_data_improper_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'Pair Coeffs'): + sys.stderr.write(' processing \"'+line.strip()+'\"\n') + some_pair_coeffs_read = True + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + if (len(tokens) < 2): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical line in Pair Coeffs section:\n' + ' \"'+line.strip()+'\"\n') + atomtype_i_str = tokens[0] + if '*' in atomtype_i_str: + raise InputError('PROBLEM near or before '+ErrorLeader(infile, lineno)+'\n' + ' As of 2012-7, moltemplate forbids use of the "\*\" wildcard\n' + ' character in the \"Pair Coeffs\" section.\n') + else: + i = int(atomtype_i_str) + if ((not i) or + BelongsToSel(i, atomtype_selection)): + i_str = '@atom:type'+str(i) + tokens[0] = i_str + l_data_pair_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (tokens[0] == 'pair_coeff'): + some_pair_coeffs_read = True + if (len(tokens) < 3): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical pair_coeff command:\n' + ' \"'+line.strip()+'\"\n') + l_in_pair_coeffs.append(' '*indent+line.strip()) + + elif (tokens[0] == 'mass'): + some_pair_coeffs_read = True + if (len(tokens) < 3): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical \"mass\" command:\n' + ' \"'+line.strip()+'\"\n') + l_in_masses.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (tokens[0] == 'bond_coeff'): + if (len(tokens) < 2): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical bond_coeff command:\n' + ' \"'+line.strip()+'\"\n') + #tokens[1] = '@bond:type'+tokens[1] + l_in_bond_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (tokens[0] == 'angle_coeff'): + if (len(tokens) < 2): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical angle_coeff command:\n' + ' \"'+line.strip()+'\"\n') + #tokens[1] = '@angle:type'+tokens[1] + l_in_angle_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (tokens[0] == 'dihedral_coeff'): + if (len(tokens) < 2): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical dihedral_coeff command:\n' + ' \"'+line.strip()+'\"\n') + #tokens[1] = '@dihedral:type'+tokens[1] + l_in_dihedral_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + elif (tokens[0] == 'improper_coeff'): + if (len(tokens) < 2): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical improper_coeff command:\n' + ' \"'+line.strip()+'\"\n') + #tokens[1] = '@improper:type'+tokens[1] + l_in_improper_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + + # -- class2 force fields -- + elif (line.strip() == 'BondBond Coeffs'): + sys.stderr.write(' processing \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@angle:type'+tokens[0] + l_data_bondbond_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'BondAngle Coeffs'): + sys.stderr.write(' processing \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@angle:type'+tokens[0] + l_data_bondangle_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'MiddleBondTorsion Coeffs'): + sys.stderr.write(' processing \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@dihedral:type'+tokens[0] + l_data_middlebondtorsion_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'EndBondTorsion Coeffs'): + sys.stderr.write(' processing \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@dihedral:type'+tokens[0] + l_data_endbondtorsion_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'AngleTorsion Coeffs'): + sys.stderr.write(' processing \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@dihedral:type'+tokens[0] + l_data_angletorsion_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'AngleAngleTorsion Coeffs'): + sys.stderr.write(' processing \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@dihedral:type'+tokens[0] + l_data_angleangletorsion_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'BondBond13 Coeffs'): + sys.stderr.write(' processing \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@dihedral:type'+tokens[0] + l_data_bondbond13_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'AngleAngle Coeffs'): + sys.stderr.write(' processing \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@improper:type'+tokens[0] + l_data_angleangle_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'Angles By Type'): + sys.stderr.write(' processing \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@angle:type'+tokens[0] + l_data_angles_by_type.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'Dihedrals By Type'): + sys.stderr.write(' processing \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@dihedral:type'+tokens[0] + l_data_dihedrals_by_type.append((' '*indent)+(' '.join(tokens)+'\n')) + + elif (line.strip() == 'Impropers By Type'): + sys.stderr.write(' processing \"'+line.strip()+'\"\n') + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + tokens[0] = '@improper:type'+tokens[0] + l_data_impropers_by_type.append((' '*indent)+(' '.join(tokens)+'\n')) + + else: + sys.stderr.write(' Ignoring line \"'+line.strip()+'\"\n') + + sys.stderr.write('\n\n') + # --- Now delete items that were not selected from the other lists --- + + # --- MASSES --- + + # delete masses for atom types we don't care about anymore: + i_line = 0 + while i_line < len(l_data_masses): + line = l_data_masses[i_line] + tokens = line.strip().split() + atomtype = Intify(tokens[0]) + if ((not (atomtype in needed_atomtypes)) and + (not ((len(atomtype_selection) > 0) and + BelongsToSel(atomtype, atomtype_selection)))): + del(l_data_masses[i_line]) + else: + tokens[0] = '@atom:type'+str(atomtype) + l_data_masses[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + + + + # --- PAIR COEFFS --- + + # delete data_pair_coeffs for atom types we don't care about anymore: + i_line = 0 + while i_line < len(l_data_pair_coeffs): + line = l_data_pair_coeffs[i_line] + tokens = line.strip().split() + assert(len(tokens) > 0) + split_colon = tokens[0].split(':') + assert(len(split_colon) == 2) + atomtype = Intify(split_colon[1]) + if ((not (atomtype in needed_atomtypes)) and + (not ((len(atomtype_selection) > 0) and + BelongsToSel(atomtype, atomtype_selection)))): + del(l_data_pair_coeffs[i_line]) + else: + i_line += 1 + + # delete in_pair_coeffs for atom we don't care about anymore: + i_line = 0 + while i_line < len(l_in_pair_coeffs): + line = l_in_pair_coeffs[i_line] + tokens = line.strip().split() + atomtype_i_str = tokens[1] + atomtype_j_str = tokens[2] + #if (('*' in atomtype_i_str) or + # ('*' in atomtype_j_str)): + # sys.stderr.write('WARNING: near or before '+ErrorLeader(infile, lineno)+'\n' + # ' pair_coeff command contains a \"*\" character.\n' + # ' Keep in mind that using moltemplate.sh you can manually change the\n' + # ' numbers assigned to each atom type (when using -a or -b). Make sure\n' + # ' nor to accidentally change the order of atom types in one of these\n' + # ' pair_coeff commands. For example, commands like\n' + # ' pair_coeff 10*4 20*10 0.15 3.6\n' + # ' can be generated by moltemplate.sh, however\n' + # ' they may be rejected by LAMMPS (because LAMMPS prefers this\n' + # ' pair_coeff 4*10 10*20 0.15 3.6)\n' + # ' Later on, you may want to check to make sure moltemplate.sh\n' + # ' is not doing this. (Fortunately you never have to worry unless\n' + # ' you are using the -a or -b arguments with moltemplate.sh)\n') + + if ('*' in atomtype_i_str): + atomtype_i_tokens = atomtype_i_str.split('*') + + if atomtype_i_tokens[0] == '': + if (min_sel_atomtype and + (min_sel_atomtype < min_needed_atomtype)): + i_a = min_sel_atomtype + else: + i_a = min_needed_atomtype + else: + i_a = Intify(atomtype_i_tokens[0]) + + if atomtype_i_tokens[1] == '': + if (max_sel_atomtype and + (max_sel_atomtype > max_needed_atomtype)): + i_b = max_sel_atomtype + else: + i_b = max_needed_atomtype + else: + i_b = Intify(atomtype_i_tokens[1]) + + else: + i_a = i_b = Intify(atomtype_i_str) + + i_a_final = None + i_b_final = None + for i in range(i_a, i_b+1): + if ((i in needed_atomtypes) or (min_sel_atomtype <= i)): + i_a_final = i + break + for i in reversed(range(i_a, i_b+1)): + if ((i in needed_atomtypes) or (max_sel_atomtype >= i)): + i_b_final = i + break + + #if i_a_final and i_b_final: + # if i_a_final == i_b_final: + # i_str = '@atom:type'+str(i_a_final) + # tokens[1] = i_str + # else: + # i_str = '@{atom:type'+str(i_a_final)+'}*@{atom:type'+str(i_b_final)+'}' + + + + if ('*' in atomtype_j_str): + atomtype_j_tokens = atomtype_j_str.split('*') + + if atomtype_j_tokens[0] == '': + if (min_sel_atomtype and + (min_sel_atomtype < min_needed_atomtype)): + j_a = min_sel_atomtype + else: + j_a = min_needed_atomtype + else: + j_a = Intify(atomtype_j_tokens[0]) + + if atomtype_j_tokens[1] == '': + if (max_sel_atomtype and + (max_sel_atomtype > max_needed_atomtype)): + j_b = max_sel_atomtype + else: + j_b = max_needed_atomtype + else: + j_b = Intify(atomtype_j_tokens[1]) + + else: + j_a = j_b = Intify(atomtype_j_str) + + j_a_final = None + j_b_final = None + for j in range(j_a, j_b+1): + if ((j in needed_atomtypes) or (min_sel_atomtype <= j)): + j_a_final = j + break + for j in reversed(range(j_a, j_b+1)): + if ((j in needed_atomtypes) or (max_sel_atomtype >= j)): + j_b_final = j + break + + #if j_a_final and j_b_final: + # if j_a_final == j_b_final: + # j_str = '@atom:type'+str(j_a_final) + # tokens[1] = j_str + # else: + # j_str = '@{atom:type'+str(j_a_final)+'}*@{atom:type'+str(j_b_final)+'}' + + + + if not (i_a_final and i_b_final and j_a_final and j_b_final): + del(l_in_pair_coeffs[i_line]) + elif (('*' in atomtype_i_str) or ('*' in atomtype_j_str)): + del(l_in_pair_coeffs[i_line]) + for i in range(i_a_final, i_b_final+1): + for j in range(j_a_final, j_b_final+1): + if j >= i: + tokens[1] = '@atom:type'+str(i) + tokens[2] = '@atom:type'+str(j) + l_in_pair_coeffs.insert(i_line, + (' '*indent)+(' '.join(tokens)+'\n')) + i_line += 1 + else: + tokens[1] = '@atom:type'+tokens[1] + tokens[2] = '@atom:type'+tokens[2] + l_in_pair_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + + + + + # delete mass commands for atom types we don't care about anymore: + i_line = 0 + while i_line < len(l_in_masses): + line = l_in_masses[i_line] + tokens = line.strip().split() + atomtype_i_str = tokens[1] + #if (('*' in atomtype_i_str) or + # ('*' in atomtype_j_str)): + # sys.stderr.write('WARNING: near or before '+ErrorLeader(infile, lineno)+'\n' + # ' pair_coeff command contains a \"*\" character.\n' + # ' Keep in mind that using moltemplate.sh you can manually change the\n' + # ' numbers assigned to each atom type (when using -a or -b). Make sure\n' + # ' nor to accidentally change the order of atom types in one of these\n' + # ' pair_coeff commands. For example, commands like\n' + # ' pair_coeff 10*4 20*10 0.15 3.6\n' + # ' can be generated by moltemplate.sh, however\n' + # ' they may be rejected by LAMMPS (because LAMMPS prefers this\n' + # ' pair_coeff 4*10 10*20 0.15 3.6)\n' + # ' Later on, you may want to check to make sure moltemplate.sh\n' + # ' is not doing this. (Fortunately you never have to worry unless\n' + # ' you are using the -a or -b arguments with moltemplate.sh)\n') + + if ('*' in atomtype_i_str): + atomtype_i_tokens = atomtype_i_str.split('*') + + if atomtype_i_tokens[0] == '': + if (min_sel_atomtype and + (min_sel_atomtype < min_needed_atomtype)): + i_a = min_sel_atomtype + else: + i_a = min_needed_atomtype + else: + i_a = Intify(atomtype_i_tokens[0]) + + if atomtype_i_tokens[1] == '': + if (max_sel_atomtype and + (max_sel_atomtype > max_needed_atomtype)): + i_b = max_sel_atomtype + else: + i_b = max_needed_atomtype + else: + i_b = Intify(atomtype_i_tokens[1]) + + else: + i_a = i_b = Intify(atomtype_i_str) + + i_a_final = None + i_b_final = None + for i in range(i_a, i_b+1): + if ((i in needed_atomtypes) or (min_sel_atomtype <= i)): + i_a_final = i + break + for i in reversed(range(i_a, i_b+1)): + if ((i in needed_atomtypes) or (max_sel_atomtype >= i)): + i_b_final = i + break + #if i_a_final and i_b_final: + # if i_a_final == i_b_final: + # i_str = '@atom:type'+str(i_a_final) + # tokens[1] = i_str + # else: + # i_str = '@{atom:type'+str(i_a_final)+'}*@{atom:type'+str(i_b_final)+'}' + + if not (i_a_final and i_b_final and j_a_final and j_b_final): + del(l_in_masses[i_line]) + elif ('*' in atomtype_i_str): + del(l_in_masses[i_line]) + for i in range(i_a_final, i_b_final+1): + tokens[1] = '@atom:type'+str(i) + l_in_masses.insert(i_line, (' '*indent)+(' '.join(tokens)+'\n')) + i_line += 1 + else: + assert(i_a == i_b) + tokens[1] = '@atom:type'+str(i_a) + l_in_masses[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + + + + + # --- BONDS AND BOND COEFFS --- + + # delete lines from data_bonds if they involve atoms we don't care about + i_line = 0 + while i_line < len(l_data_bonds): + line = l_data_bonds[i_line] + tokens = line.strip().split() + assert(len(tokens) == 4) + + bondid = Intify(tokens[0]) + bondtype = Intify(tokens[1]) + atomid1 = Intify(tokens[2]) + atomid2 = Intify(tokens[3]) + #if ((atomid1 in needed_atomids) and + # (atomid2 in needed_atomids)): + tokens[0] = '$bond:id'+str(bondid) + tokens[1] = '@bond:type'+str(bondtype) + tokens[2] = '$atom:id'+str(atomid1) + tokens[3] = '$atom:id'+str(atomid2) + needed_bondids.add(bondid) + needed_bondtypes.add(bondtype) + l_data_bonds[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + #else: + # del(l_data_bonds[i_line]) + + # delete data_bond_coeffs for bondtypes we don't care about anymore: + i_line = 0 + while i_line < len(l_data_bond_coeffs): + line = l_data_bond_coeffs[i_line] + tokens = line.strip().split() + bondtype = Intify(tokens[0]) + if (not (bondtype in needed_bondtypes)): + del(l_data_bond_coeffs[i_line]) + else: + tokens[0] = '@bond:type'+str(bondtype) + l_data_bond_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + + # delete in_bond_coeffs for bondtypes we don't care about anymore: + for bondtype in needed_bondtypes: + if type(bondtype) is int: + if ((min_needed_bondtype == None) or + (min_needed_bondtype > bondtype)): + min_needed_bondtype = bondtype + if ((max_needed_bondtype == None) or + (max_needed_bondtype < bondtype)): + max_needed_bondtype = bondtype + i_line = 0 + while i_line < len(l_in_bond_coeffs): + line = l_in_bond_coeffs[i_line] + tokens = line.strip().split() + bondtype_str = tokens[1] + + if ('*' in bondtype_str): + bondtype_tokens = bondtype_str.split('*') + + if bondtype_tokens[0] == '': + i_a = min_needed_bondtype + else: + i_a = Intify(bondtype_tokens[0]) + + if bondtype_tokens[1] == '': + i_b = max_needed_bondtype + else: + i_b = Intify(bondtype_tokens[1]) + + else: + i_a = i_b = Intify(bondtype_str) + + if i_a < min_needed_bondtype: + i_a = min_needed_bondtype + if i_b > max_needed_bondtype: + i_b = max_needed_bondtype + + #if i_a == i_b: + # i_str = '@bond:type'+str(i_a) + # tokens[1] = i_str + #else: + # i_str = '@{bond:type'+str(j_a)+'}*@{bond:type'+str(j_b)+'}' + + if ('*' in bondtype_str): + del(l_in_bond_coeffs[i_line]) + for i in range(i_a, i_b+1): + if (i in needed_bondtypes): + tokens[1] = '@bond:type'+str(i) + l_in_bond_coeffs.insert(i_line, + (' '*indent)+(' '.join(tokens)+'\n')) + i_line += 1 + else: + assert(i_a == i_b) + if (i_a in needed_bondtypes): + tokens[1] = '@bond:type'+str(i_a) + l_in_bond_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + else: + del(l_in_bond_coeffs[i_line]) + + + + + + # --- ANGLES AND ANGLE COEFFS --- + + # delete lines from data_angles if they involve atoms we don't care about + i_line = 0 + while i_line < len(l_data_angles): + line = l_data_angles[i_line] + tokens = line.strip().split() + assert(len(tokens) == 5) + + angleid = Intify(tokens[0]) + angletype = Intify(tokens[1]) + atomid1 = Intify(tokens[2]) + atomid2 = Intify(tokens[3]) + atomid3 = Intify(tokens[4]) + #if ((atomid1 in needed_atomids) and + # (atomid2 in needed_atomids)): + tokens[0] = '$angle:id'+str(angleid) + tokens[1] = '@angle:type'+str(angletype) + tokens[2] = '$atom:id'+str(atomid1) + tokens[3] = '$atom:id'+str(atomid2) + tokens[4] = '$atom:id'+str(atomid3) + needed_angleids.add(angleid) + needed_angletypes.add(angletype) + l_data_angles[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + #else: + # del(l_data_angles[i_line]) + + # delete data_angle_coeffs for angletypes we don't care about anymore: + i_line = 0 + while i_line < len(l_data_angle_coeffs): + line = l_data_angle_coeffs[i_line] + tokens = line.strip().split() + angletype = Intify(tokens[0]) + if (not (angletype in needed_angletypes)): + del(l_data_angle_coeffs[i_line]) + else: + tokens[0] = '@angle:type'+str(angletype) + l_data_angle_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + + # delete in_angle_coeffs for angletypes we don't care about anymore: + for angletype in needed_angletypes: + if type(angletype) is int: + if ((min_needed_angletype == None) or + (min_needed_angletype > angletype)): + min_needed_angletype = angletype + if ((max_needed_angletype == None) or + (max_needed_angletype < angletype)): + max_needed_angletype = angletype + i_line = 0 + while i_line < len(l_in_angle_coeffs): + line = l_in_angle_coeffs[i_line] + tokens = line.strip().split() + angletype_str = tokens[1] + + if ('*' in angletype_str): + angletype_tokens = angletype_str.split('*') + + if angletype_tokens[0] == '': + i_a = min_needed_angletype + else: + i_a = Intify(angletype_tokens[0]) + + if angletype_tokens[1] == '': + i_b = max_needed_angletype + else: + i_b = Intify(angletype_tokens[1]) + + else: + i_a = i_b = Intify(angletype_str) + + if i_a < min_needed_angletype: + i_a = min_needed_angletype + if i_b > max_needed_angletype: + i_b = max_needed_angletype + + #if i_a == i_b: + # i_str = '@angle:type'+str(i_a) + # tokens[1] = i_str + #else: + # i_str = '@{angle:type'+str(j_a)+'}*@{angle:type'+str(j_b)+'}' + + if ('*' in angletype_str): + del(l_in_angle_coeffs[i_line]) + for i in range(i_a, i_b+1): + if (i in needed_angletypes): + tokens[1] = '@angle:type'+str(i) + l_in_angle_coeffs.insert(i_line, + (' '*indent)+(' '.join(tokens)+'\n')) + i_line += 1 + else: + assert(i_a == i_b) + if (i_a in needed_angletypes): + tokens[1] = '@angle:type'+str(i_a) + l_in_angle_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + else: + del(l_in_angle_coeffs[i_line]) + + + + # --- DIHEDRALS AND DIHEDRAL COEFFS --- + + # delete lines from data_dihedrals if they involve atoms we don't care about + i_line = 0 + while i_line < len(l_data_dihedrals): + line = l_data_dihedrals[i_line] + tokens = line.strip().split() + assert(len(tokens) == 6) + + dihedralid = Intify(tokens[0]) + dihedraltype = Intify(tokens[1]) + atomid1 = Intify(tokens[2]) + atomid2 = Intify(tokens[3]) + atomid3 = Intify(tokens[4]) + atomid4 = Intify(tokens[5]) + #if ((atomid1 in needed_atomids) and + # (atomid2 in needed_atomids)): + tokens[0] = '$dihedral:id'+str(dihedralid) + tokens[1] = '@dihedral:type'+str(dihedraltype) + tokens[2] = '$atom:id'+str(atomid1) + tokens[3] = '$atom:id'+str(atomid2) + tokens[4] = '$atom:id'+str(atomid3) + tokens[5] = '$atom:id'+str(atomid4) + needed_dihedralids.add(dihedralid) + needed_dihedraltypes.add(dihedraltype) + l_data_dihedrals[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + #else: + # del(l_data_dihedrals[i_line]) + + # delete data_dihedral_coeffs for dihedraltypes we don't care about anymore: + i_line = 0 + while i_line < len(l_data_dihedral_coeffs): + line = l_data_dihedral_coeffs[i_line] + tokens = line.strip().split() + dihedraltype = Intify(tokens[0]) + if (not (dihedraltype in needed_dihedraltypes)): + del(l_data_dihedral_coeffs[i_line]) + else: + tokens[0] = '@dihedral:type'+str(dihedraltype) + l_data_dihedral_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + + # delete in_dihedral_coeffs for dihedraltypes we don't care about anymore: + for dihedraltype in needed_dihedraltypes: + if type(dihedraltype) is int: + if ((min_needed_dihedraltype == None) or + (min_needed_dihedraltype > dihedraltype)): + min_needed_dihedraltype = dihedraltype + if ((max_needed_dihedraltype == None) or + (max_needed_dihedraltype < dihedraltype)): + max_needed_dihedraltype = dihedraltype + i_line = 0 + while i_line < len(l_in_dihedral_coeffs): + line = l_in_dihedral_coeffs[i_line] + tokens = line.strip().split() + dihedraltype_str = tokens[1] + + if ('*' in dihedraltype_str): + dihedraltype_tokens = dihedraltype_str.split('*') + + if dihedraltype_tokens[0] == '': + i_a = min_needed_dihedraltype + else: + i_a = Intify(dihedraltype_tokens[0]) + + if dihedraltype_tokens[1] == '': + i_b = max_needed_dihedraltype + else: + i_b = Intify(dihedraltype_tokens[1]) + + else: + i_a = i_b = Intify(dihedraltype_str) + + if i_a < min_needed_dihedraltype: + i_a = min_needed_dihedraltype + if i_b > max_needed_dihedraltype: + i_b = max_needed_dihedraltype + + #if i_a == i_b: + # i_str = '@dihedral:type'+str(i_a) + # tokens[1] = i_str + #else: + # i_str = '@{dihedral:type'+str(j_a)+'}*@{dihedral:type'+str(j_b)+'}' + + if ('*' in dihedraltype_str): + del(l_in_dihedral_coeffs[i_line]) + for i in range(i_a, i_b+1): + if (i in needed_dihedraltypes): + tokens[1] = '@dihedral:type'+str(i) + l_in_dihedral_coeffs.insert(i_line, + (' '*indent)+(' '.join(tokens)+'\n')) + i_line += 1 + else: + assert(i_a == i_b) + if (i_a in needed_dihedraltypes): + tokens[1] = '@dihedral:type'+str(i_a) + l_in_dihedral_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + else: + del(l_in_dihedral_coeffs[i_line]) + + + + # --- IMPROPERS AND IMPROPER COEFFS --- + + # delete lines from data_impropers if they involve atoms we don't care about + i_line = 0 + while i_line < len(l_data_impropers): + line = l_data_impropers[i_line] + tokens = line.strip().split() + assert(len(tokens) == 6) + + improperid = Intify(tokens[0]) + impropertype = Intify(tokens[1]) + atomid1 = Intify(tokens[2]) + atomid2 = Intify(tokens[3]) + atomid3 = Intify(tokens[4]) + atomid4 = Intify(tokens[5]) + #if ((atomid1 in needed_atomids) and + # (atomid2 in needed_atomids)): + tokens[0] = '$improper:id'+str(improperid) + tokens[1] = '@improper:type'+str(impropertype) + tokens[2] = '$atom:id'+str(atomid1) + tokens[3] = '$atom:id'+str(atomid2) + tokens[4] = '$atom:id'+str(atomid3) + tokens[5] = '$atom:id'+str(atomid4) + needed_improperids.add(improperid) + needed_impropertypes.add(impropertype) + l_data_impropers[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + #else: + # del(l_data_impropers[i_line]) + + # delete data_improper_coeffs for impropertypes we don't care about anymore: + i_line = 0 + while i_line < len(l_data_improper_coeffs): + line = l_data_improper_coeffs[i_line] + tokens = line.strip().split() + impropertype = Intify(tokens[0]) + if (not (impropertype in needed_impropertypes)): + del(l_data_improper_coeffs[i_line]) + else: + tokens[0] = '@improper:type'+str(impropertype) + l_data_improper_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + + # delete in_improper_coeffs for impropertypes we don't care about anymore: + for impropertype in needed_impropertypes: + if type(impropertype) is int: + if ((min_needed_impropertype == None) or + (min_needed_impropertype > impropertype)): + min_needed_impropertype = impropertype + if ((max_needed_impropertype == None) or + (max_needed_impropertype < impropertype)): + max_needed_impropertype = impropertype + i_line = 0 + while i_line < len(l_in_improper_coeffs): + line = l_in_improper_coeffs[i_line] + tokens = line.strip().split() + impropertype_str = tokens[1] + + if ('*' in impropertype_str): + impropertype_tokens = impropertype_str.split('*') + + if impropertype_tokens[0] == '': + i_a = min_needed_impropertype + else: + i_a = Intify(impropertype_tokens[0]) + + if impropertype_tokens[1] == '': + i_b = max_needed_impropertype + else: + i_b = Intify(impropertype_tokens[1]) + + else: + i_a = i_b = Intify(impropertype_str) + + if i_a < min_needed_impropertype: + i_a = min_needed_impropertype + if i_b > max_needed_impropertype: + i_b = max_needed_impropertype + + #if i_a == i_b: + # i_str = '@improper:type'+str(i_a) + # tokens[1] = i_str + #else: + # i_str = '@{improper:type'+str(j_a)+'}*@{improper:type'+str(j_b)+'}' + + if ('*' in impropertype_str): + del(l_in_improper_coeffs[i_line]) + for i in range(i_a, i_b+1): + if (i in needed_impropertypes): + tokens[1] = '@improper:type'+str(i) + l_in_improper_coeffs.insert(i_line, + (' '*indent)+(' '.join(tokens)+'\n')) + i_line += 1 + else: + assert(i_a == i_b) + if (i_a in needed_impropertypes): + tokens[1] = '@improper:type'+str(i_a) + l_in_improper_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + else: + del(l_in_improper_coeffs[i_line]) + + + + + + + + + if not some_pair_coeffs_read: + sys.stderr.write('Warning: No \"pair coeffs\" set.\n' + ' (No interactions between non-bonded atoms defined.)\n') + no_warnings = False + + #sys.stderr.write('Writing ttree data to standard out.\n' + # ' You can redirect this to a file using:\n'+ + # ' '+' '.join(sys.argv)+' > filename.ttree\n' + # ' ----------------------\n') + + if mol_name != '': + sys.stdout.write(mol_name + ' {\n') + + if len(l_in_init) > 0: + sys.stdout.write('\n### LAMMPS commands for initialization\n' + '### (These can be overridden later.)\n\n') + l_in_init.insert(0, (' '*cindent)+'write_once(\"'+in_init+'\") {\n') + l_in_init.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_in_init)) + if len(l_in_settings) > 0: + sys.stdout.write('\n### LAMMPS commands for settings\n' + '### (These can be overridden later.)\n\n') + l_in_settings.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') + l_in_settings.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_in_settings)) + non_empty_output = True + if len(l_in_masses) > 0: + l_in_masses.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') + l_in_masses.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_in_masses)) + non_empty_output = True + if len(l_in_pair_coeffs) > 0: + l_in_pair_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') + l_in_pair_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_in_pair_coeffs)) + non_empty_output = True + if len(l_in_bond_coeffs) > 0: + l_in_bond_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') + l_in_bond_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_in_bond_coeffs)) + non_empty_output = True + if len(l_in_angle_coeffs) > 0: + l_in_angle_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') + l_in_angle_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_in_angle_coeffs)) + non_empty_output = True + if len(l_in_dihedral_coeffs) > 0: + l_in_dihedral_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') + l_in_dihedral_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_in_dihedral_coeffs)) + non_empty_output = True + if len(l_in_improper_coeffs) > 0: + l_in_improper_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') + l_in_improper_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_in_improper_coeffs)) + non_empty_output = True + + if non_empty_output: + sys.stdout.write('\n### DATA sections\n\n') + + if len(l_data_masses) > 0: + l_data_masses.insert(0, (' '*cindent)+'write_once(\"'+data_masses+'\") {\n') + l_data_masses.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_masses)) + non_empty_output = True + if len(l_data_bond_coeffs) > 0: + l_data_bond_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_bond_coeffs+'\") {\n') + l_data_bond_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_bond_coeffs)) + non_empty_output = True + if len(l_data_angle_coeffs) > 0: + l_data_angle_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_angle_coeffs+'\") {\n') + l_data_angle_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_angle_coeffs)) + non_empty_output = True + if len(l_data_dihedral_coeffs) > 0: + l_data_dihedral_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_dihedral_coeffs+'\") {\n') + l_data_dihedral_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_dihedral_coeffs)) + non_empty_output = True + if len(l_data_improper_coeffs) > 0: + l_data_improper_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_improper_coeffs+'\") {\n') + l_data_improper_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_improper_coeffs)) + non_empty_output = True + if len(l_data_pair_coeffs) > 0: + l_data_pair_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_pair_coeffs+'\") {\n') + l_data_pair_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_pair_coeffs)) + non_empty_output = True + + # class2 force fields: + if len(l_data_bondbond_coeffs) > 0: + l_data_bondbond_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_bondbond_coeffs+'\") {\n') + l_data_bondbond_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_bondbond_coeffs)) + non_empty_output = True + if len(l_data_bondangle_coeffs) > 0: + l_data_bondangle_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_bondangle_coeffs+'\") {\n') + l_data_bondangle_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_bondangle_coeffs)) + non_empty_output = True + if len(l_data_middlebondtorsion_coeffs) > 0: + l_data_middlebondtorsion_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_middlebondtorsion_coeffs+'\") {\n') + l_data_middlebondtorsion_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_middlebondtorsion_coeffs)) + non_empty_output = True + if len(l_data_endbondtorsion_coeffs) > 0: + l_data_endbondtorsion_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_endbondtorsion_coeffs+'\") {\n') + l_data_endbondtorsion_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_endbondtorsion_coeffs)) + non_empty_output = True + if len(l_data_angletorsion_coeffs) > 0: + l_data_angletorsion_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_angletorsion_coeffs+'\") {\n') + l_data_angletorsion_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_angletorsion_coeffs)) + non_empty_output = True + if len(l_data_angleangletorsion_coeffs) > 0: + l_data_angleangletorsion_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_angleangletorsion_coeffs+'\") {\n') + l_data_angleangletorsion_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_angleangletorsion_coeffs)) + non_empty_output = True + if len(l_data_bondbond13_coeffs) > 0: + l_data_bondbond13_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_bondbond13_coeffs+'\") {\n') + l_data_bondbond13_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_bondbond13_coeffs)) + non_empty_output = True + if len(l_data_angleangle_coeffs) > 0: + l_data_angleangle_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_angleangle_coeffs+'\") {\n') + l_data_angleangle_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_angleangle_coeffs)) + non_empty_output = True + + # automatic generation of bonded interactions by type: + if len(l_data_angles_by_type) > 0: + l_data_angles_by_type.insert(0, (' '*cindent)+'write_once(\"'+data_angles_by_type+'\") {\n') + l_data_angles_by_type.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_angles_by_type)) + non_empty_output = True + if len(l_data_dihedrals_by_type) > 0: + l_data_dihedrals_by_type.insert(0, (' '*cindent)+'write_once(\"'+data_dihedrals_by_type+'\") {\n') + l_data_dihedrals_by_type.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_dihedrals_by_type)) + non_empty_output = True + if len(l_data_impropers_by_type) > 0: + l_data_impropers_by_type.insert(0, (' '*cindent)+'write_once(\"'+data_impropers_by_type+'\") {\n') + l_data_impropers_by_type.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_impropers_by_type)) + non_empty_output = True + + if len(l_data_atoms) > 0: + l_data_atoms.insert(0, (' '*cindent)+'write(\"'+data_atoms+'\") {\n') + l_data_atoms.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_atoms)) + non_empty_output = True + else: + sys.stderr.write('Warning: missing \"Atoms\" section.\n' + ' (Did you include a LAMMPS data file in your argument list?)\n') + no_warnings = False + + # non-point-like particles + if len(l_data_ellipsoids) > 0: + l_data_ellipsoids.insert(0, (' '*cindent)+'write(\"'+data_ellipsoids+'\") {\n') + l_data_ellipsoids.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_ellipsoids)) + if len(l_data_lines) > 0: + l_data_lines.insert(0, (' '*cindent)+'write(\"'+data_lines+'\") {\n') + l_data_lines.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_lines)) + if len(l_data_triangles) > 0: + l_data_triangles.insert(0, (' '*cindent)+'write(\"'+data_triangles+'\") {\n') + l_data_triangles.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_triangles)) + + if len(l_data_velocities) > 0: + l_data_velocities.insert(0, (' '*cindent)+'write(\"'+data_velocities+'\") {\n') + l_data_velocities.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_velocities)) + if len(l_data_bonds) > 0: + l_data_bonds.insert(0, (' '*cindent)+'write(\"'+data_bonds+'\") {\n') + l_data_bonds.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_bonds)) + non_empty_output = True + if len(l_data_angles) > 0: + l_data_angles.insert(0, (' '*cindent)+'write(\"'+data_angles+'\") {\n') + l_data_angles.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_angles)) + non_empty_output = True + if len(l_data_dihedrals) > 0: + l_data_dihedrals.insert(0, (' '*cindent)+'write(\"'+data_dihedrals+'\") {\n') + l_data_dihedrals.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_dihedrals)) + non_empty_output = True + if len(l_data_impropers) > 0: + l_data_impropers.insert(0, (' '*cindent)+'write(\"'+data_impropers+'\") {\n') + l_data_impropers.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_impropers)) + non_empty_output = True + + if mol_name != '': + sys.stdout.write('\n} # end of \"'+mol_name+'\" type definition\n') + + if non_empty_output and no_warnings: + sys.stderr.write('WARNING: The '+g_program_name+' script has not been rigorously tested.\n' + ' Exotic (manybody) pair styles (and other force-field styles\n' + ' with unusual syntax) are not understood by '+g_program_name+'\n' + ' (although they are supported by moltemplate). Please look over\n' + ' the resulting LT file and check for errors. Convert any remaining\n' + ' atom, bond, angle, dihedral, or improper id or type numbers to the\n' + ' corresponding variables. Feel free to report any bugs you find.\n' + ' (-Andrew Jewett 2012-12-11)\n') + +except (ValueError, InputError) as err: + sys.stderr.write('\n'+str(err)+'\n') + sys.exit(-1) diff --git a/tools/moltemplate/src/lttree.py b/tools/moltemplate/src/lttree.py new file mode 100755 index 0000000000..1c7a655283 --- /dev/null +++ b/tools/moltemplate/src/lttree.py @@ -0,0 +1,745 @@ +#!/usr/bin/env python + +# Author: Andrew Jewett (jewett.aij at g mail) +# http://www.chem.ucsb.edu/~sheagroup +# License: 3-clause BSD License (See LICENSE.TXT) +# Copyright (c) 2011, Regents of the University of California +# All rights reserved. + +""" +lttree.py + +lttree.py is an extension of the generic ttree.py program. +This version can understand and manipulate ttree-style templates which +are specialized for storing molecule-specific data for use in LAMMPS. + +The main difference between lttree.py and ttree.py is: +Unlike ttree.py, lttree.py understands rigid-body movement commands like +"rot()" and "move()" which allows it to reorient and move each copy +of a molecule to a new location. (ttree.py just ignores these commands. +Consequently LAMMPS input file (fragments) created with ttree.py have +invalid (overlapping) atomic coordinates and must be modified or aguemted +later (by loading atomic coordinates from a PDB file or an XYZ file). +lttree.py understands the "Data Atoms" section of a LAMMPS +data file (in addition to the various "atom_styles" which effect it). + +Additional LAMMPS-specific features may be added in the future. + +""" + +import sys +from ttree import * +from lttree_styles import * +from ttree_matrix_stack import * + +try: + unicode +except NameError: + # Python 3 + basestring = unicode = str + + + + +class LttreeSettings(BasicUISettings): + def __init__(self, + user_bindings_x=None, + user_bindings=None, + order_method='by_command'): + + BasicUISettings.__init__(self, + user_bindings_x, + user_bindings, + order_method) + + # The following new member data indicate which columns store + # LAMMPS-specific information. + # The next 6 members store keep track of the different columns + # of the "Data Atoms" section of a LAMMPS data file: + self.column_names = [] #<--A list of column names (optional) + self.ii_coords=[] #<--A list of triplets of column indexes storing coordinate data + self.ii_vects=[] #<--A list of triplets of column indexes storing directional data + # (such as dipole or ellipsoid orientations) + self.i_atomid=None #<--An integer indicating which column has the atomid + self.i_atomtype=None #<--An integer indicating which column has the atomtype + self.i_molid=None #<--An integer indicating which column has the molid, if applicable + self.infile=None # Name of the outermost file. This is the file + # which was read at the moment parsing begins. + + + + +def LttreeParseArgs(argv, settings): + + BasicUIParseArgs(argv, settings) + + # Loop over the remaining arguments not processed yet. + # These arguments are specific to the lttree.py program + # and are not understood by ttree.py: + i = 1 + while i < len(argv): + #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n') + if ((argv[i].lower() == '-atomstyle') or + (argv[i].lower() == '-atom-style') or + (argv[i].lower() == '-atom_style')): + if i+1 >= len(argv): + raise InputError('Error('+g_program_name+'): The '+argv[i]+' flag should be followed by a LAMMPS\n' + ' atom_style name (or single quoted string containing a space-separated\n' + ' list of column names such as: atom-ID atom-type q x y z molecule-ID.)\n') + settings.column_names = AtomStyle2ColNames(argv[i+1]) + sys.stderr.write('\n \"'+data_atoms+'\" column format:\n') + sys.stderr.write(' '+(' '.join(settings.column_names))+'\n\n') + settings.ii_coords = ColNames2Coords(settings.column_names) + settings.ii_vects = ColNames2Vects(settings.column_names) + settings.i_atomid, settings.i_atomtype, settings.i_molid = ColNames2AidAtypeMolid(settings.column_names) + del(argv[i:i+2]) + elif (argv[i].lower() == '-icoord'): + if i+1 >= len(argv): + raise InputError('Error: '+argv[i]+' flag should be followed by list of integers\n' + ' corresponding to column numbers for coordinates in\n' + ' the \"'+data_atoms+'\" section of a LAMMPS data file.\n') + ilist = argv[i+1].split() + if (len(ilist) % 3) != 0: + raise InputError('Error: '+argv[i]+' flag should be followed by list of integers.\n' + ' This is usually a list of 3 integers, but it can contain more.\n' + ' The number of cooridnate columns must be divisible by 3,\n' + ' (even if the simulation is in 2 dimensions)\n') + settings.iaffinevects = [] + for i in range(0, len(ilist)/3): + cols = [int(ilist[3*i])+1, + int(ilist[3*i+1])+1, + int(ilist[3*i+2])+1] + settings.iaffinevects.append(cols) + del(argv[i:i+2]) + elif (argv[i].lower() == '-ivect'): + if i+1 >= len(argv): + raise InputError('Error: '+argv[i]+' flag should be followed by list of integers\n' + ' corresponding to column numbers for direction vectors in\n' + ' the \"'+data_atoms+'\" section of a LAMMPS data file.\n') + ilist = argv[i+1].split() + if (len(ilist) % 3) != 0: + raise InputError('Error: '+argv[i]+' flag should be followed by list of integers.\n' + ' This is usually a list of 3 integers, but it can contain more.\n' + ' The number of cooridnate columns must be divisible by 3,\n' + ' (even if the simulation is in 2 dimensions)\n') + settings.ivects = [] + for i in range(0, len(ilist)/3): + cols = [int(ilist[3*i])+1, + int(ilist[3*i+1])+1, + int(ilist[3*i+2])+1] + settings.ivects.append(cols) + del(argv[i:i+2]) + elif ((argv[i].lower() == '-iatomid') or + (argv[i].lower() == '-iid') or + (argv[i].lower() == '-iatom-id')): + if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))): + raise InputError('Error: '+argv[i]+' flag should be followed by an integer\n' + ' (>=1) indicating which column in the \"'+data_atoms+'\" section of a\n' + ' LAMMPS data file contains the atom id number (typically 1).\n' + ' (This argument is unnecessary if you use the -atomstyle argument.)\n') + i_atomid = int(argv[i+1])-1 + del(argv[i:i+2]) + elif ((argv[i].lower() == '-iatomtype') or + (argv[i].lower() == '-itype') or + (argv[i].lower() == '-iatom-type')): + if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))): + raise InputError('Error: '+argv[i]+' flag should be followed by an integer\n' + ' (>=1) indicating which column in the \"'+data_atoms+'\" section of a\n' + ' LAMMPS data file contains the atom type.\n' + ' (This argument is unnecessary if you use the -atomstyle argument.)\n') + i_atomtype = int(argv[i+1])-1 + del(argv[i:i+2]) + elif ((argv[i].lower() == '-imolid') or + (argv[i].lower() == '-imol') or + (argv[i].lower() == '-imol-id') or + (argv[i].lower() == '-imoleculeid') or + (argv[i].lower() == '-imolecule-id')): + if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))): + raise InputError('Error: '+argv[i]+' flag should be followed by an integer\n' + ' (>=1) indicating which column in the \"'+data_atoms+'\" section of a\n' + ' LAMMPS data file contains the molecule id number.\n' + ' (This argument is unnecessary if you use the -atomstyle argument.)\n') + i_molid = int(argv[i+1])-1 + del(argv[i:i+2]) + + elif ((argv[i][0] == '-') and (__name__ == "__main__")): + #elif (__name__ == "__main__"): + raise InputError('Error('+g_program_name+'):\n' + 'Unrecogized command line argument \"'+argv[i]+'\"\n') + else: + i += 1 + + + if __name__ == "__main__": + + # Instantiate the lexer we will be using. + # (The lexer's __init__() function requires an openned file. + # Assuming __name__ == "__main__", then the name of that file should + # be the last remaining (unprocessed) argument in the argument list. + # Otherwise, then name of that file will be determined later by the + # python script which imports this module, so we let them handle it.) + + if len(argv) == 1: + raise InputError('Error: This program requires at least one argument\n' + ' the name of a file containing ttree template commands\n') + elif len(argv) == 2: + try: + settings.lex = TemplateLexer(open(argv[1], 'r'), argv[1]) # Parse text from file + except IOError: + sys.stderr.write('Error: unable to open file\n' + ' \"'+argv[1]+'\"\n' + ' for reading.\n') + sys.exit(1) + del(argv[1:2]) + + else: + # if there are more than 2 remaining arguments, + problem_args = ['\"'+arg+'\"' for arg in argv[1:]] + raise InputError('Syntax Error('+g_program_name+'):\n\n' + ' Problem with argument list.\n' + ' The remaining arguments are:\n\n' + ' '+(' '.join(problem_args))+'\n\n' + ' (The actual problem may be earlier in the argument list.\n' + ' If these arguments are source files, then keep in mind\n' + ' that this program can not parse multiple source files.)\n' + ' Check the syntax of the entire argument list.\n') + + + + if len(settings.ii_coords) == 0: + sys.stderr.write('########################################################\n' + '## WARNING: atom_style unspecified ##\n' + '## --> \"'+data_atoms+'\" column data has an unknown format ##\n' + '## Assuming atom_style = \"full\" ##\n' + # '########################################################\n' + # '## To specify the \"'+data_atoms+'\" column format you can: ##\n' + # '## 1) Use the -atomstyle \"STYLE\" argument ##\n' + # '## where \"STYLE\" is a string indicating a LAMMPS ##\n' + # '## atom_style, including hybrid styles.(Standard ##\n' + # '## atom styles defined in 2011 are supported.) ##\n' + # '## 2) Use the -atomstyle \"COL_LIST\" argument ##\n' + # '## where \"COL_LIST" is a quoted list of strings ##\n' + # '## indicating the name of each column. ##\n' + # '## Names \"x\",\"y\",\"z\" are interpreted as ##\n' + # '## atomic coordinates. \"mux\",\"muy\",\"muz\" ##\n' + # '## are interpreted as direction vectors. ##\n' + # '## 3) Use the -icoord \"cx cy cz...\" argument ##\n' + # '## where \"cx cy cz\" is a list of integers ##\n' + # '## indicating the column numbers for the x,y,z ##\n' + # '## coordinates of each atom. ##\n' + # '## 4) Use the -ivect \"cmux cmuy cmuz...\" argument ##\n' + # '## where \"cmux cmuy cmuz...\" is a list of ##\n' + # '## integers indicating the column numbers for ##\n' + # '## the vector that determines the direction of a ##\n' + # '## dipole or ellipsoid (ie. a rotateable vector).##\n' + # '## (More than one triplet can be specified. The ##\n' + # '## number of entries must be divisible by 3.) ##\n' + '########################################################\n') + + # The default atom_style is "full" + settings.column_names = AtomStyle2ColNames('full') + settings.ii_coords = ColNames2Coords(settings.column_names) + settings.ii_vects = ColNames2Vects(settings.column_names) + settings.i_atomid, settings.i_atomtype, settings.i_molid = ColNames2AidAtypeMolid(settings.column_names) + + + + + + + + + +def TransformAtomText(text, matrix): + """ Apply transformations to the coordinates and other vector degrees + of freedom stored in the \"Data Atoms\" section of a LAMMPS data file. + This is the \"text\" argument. + The \"matrix\" stores the aggregate sum of combined transformations + to be applied. + + """ + + #sys.stderr.write('matrix_stack.M = \n'+ MatToStr(matrix) + '\n') + + lines = text.split('\n') + + for i in range(0, len(lines)): + line_orig = lines[i] + ic = line_orig.find('#') + if ic != -1: + line = line_orig[:ic] + comment = ' '+line_orig[ic:].rstrip('\n') + else: + line = line_orig.rstrip('\n') + comment = '' + + columns = line.split() + if len(columns) > 0: + if len(columns) == len(settings.column_names)+3: + raise InputError('Error: lttree.py does not yet support integer unit-cell counters \n' + ' within the \"'+data_atoms+'\" section of a LAMMPS data file.\n' + ' Instead please add the appropriate offsets (these offsets\n' + ' should be multiples of the cell size) to the atom coordinates\n' + ' in the data file, and eliminate the extra columns. Then try again.\n' + ' (If you get this message often, email me and I\'ll fix this limitation.)') + if len(columns) < len(settings.column_names): + raise InputError('Error: The number of columns in your data file does not\n' + ' match the LAMMPS atom_style you selected.\n' + ' Use the -atomstyle