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tools/moltemplate/LICENSE.TXT
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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.

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tools/moltemplate/README.TXT
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-- 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.)

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tools/moltemplate/common/graphene.lt
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# 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)

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tools/moltemplate/common/spce.lt
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# 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

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tools/moltemplate/common/spce_ice_rect8.lt
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# 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).

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tools/moltemplate/common/tip3p_attempts/README.TXT
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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

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tools/moltemplate/common/tip3p_attempts/tip3p2004.lt
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# 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

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tools/moltemplate/common/tip3p_attempts/tip3pcharmm.lt
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# 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

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tools/moltemplate/common/trappe1998.lt
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# 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

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tools/moltemplate/common/watmw.lt
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# 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

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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

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# --- 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)

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# 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 ../

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------- 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.)

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254
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# 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)

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### 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)

198
tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/CGLipidBr2005.lt
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@ -1,198 +0,0 @@
# 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.)

34
tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py
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#!/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))

70
tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py
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@ -1,70 +0,0 @@
#!/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))

207
tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/system.lt
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@ -1,207 +0,0 @@
# 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"
}

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# -------- 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 --
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

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# -------- 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

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# -------- 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

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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

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# --- 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)

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# 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 ../

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------- 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.)

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# 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.)

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#!/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))

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#!/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))

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# 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)
#

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28
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# -- 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

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# -------- 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

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# ------------------------------- 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

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# 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

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# 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

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# 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

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# 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 ../

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------- 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.)

86
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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

BIN
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tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated.lt
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# 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

85
tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated_variants.lt
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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

41
tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/chaperonin.lt
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# 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.

87
tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py
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#!/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))

67
tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_dihedral_table.py
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#!/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))

45
tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/system.lt
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@ -1,45 +0,0 @@
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)
}

1188
tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat
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1187
tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat
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735
tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_dihedral_frustrated.dat
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@ -1,735 +0,0 @@
# 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 0.030335275675
49 48.0 -5.90793817411 0.0280229658805
50 49.0 -5.93480025113 0.0256996775336
51 50.0 -5.95933515063 0.0233692547166
52 51.0 -5.98153767519 0.0210355766777
53 52.0 -6.00140652074 0.0187025495211
54 53.0 -6.01894429926 0.016374097773
55 54.0 -6.03415755288 0.0140541558448
56 55.0 -6.04705675953 0.0117466594146
57 56.0 -6.05765632981 0.00945553674764
58 57.0 -6.06597459526 0.00718469997761
59 58.0 -6.07203378786 0.00493803637051
60 59.0 -6.07586001075 0.00271939959245
61 60.0 -6.07748320034 0.000532601003776
62 61.0 -6.07693707962 -0.00161859899905
63 62.0 -6.07425910291 -0.00373049957158
64 63.0 -6.06949039207 -0.00579946791801
65 64.0 -6.06267566421 -0.00782194767468
66 65.0 -6.05386315117 -0.00979446715893
67 66.0 -6.04310451074 -0.0117136474624
68 67.0 -6.03045472992 -0.0135762103679
69 68.0 -6.01597202036 -0.0153789860691
70 69.0 -5.99971770618 -0.0171189206741
71 70.0 -5.98175610439 -0.0187930834719
72 71.0 -5.9621543982 -0.0203986739443
73 72.0 -5.9409825034 -0.0219330285036
74 73.0 -5.91831292823 -0.0233936269399
75 74.0 -5.89422062685 -0.0247780985587
76 75.0 -5.86878284696 -0.0260842279959
77 76.0 -5.84207897162 -0.0273099606906
78 77.0 -5.81419035593 -0.0284534080045
79 78.0 -5.78520015867 -0.0295128519729
80 79.0 -5.7551931694 -0.0304867496727
81 80.0 -5.72425563141 -0.0313737371989
82 81.0 -5.6924750609 -0.0321726332348
83 82.0 -5.65994006273 -0.0328824422092
84 83.0 -5.62674014332 -0.0335023570292
85 84.0 -5.59296552097 -0.0340317613814
86 85.0 -5.55870693409 -0.0344702315961
87 86.0 -5.52405544786 -0.0348175380654
88 87.0 -5.48910225957 -0.0350736462148
89 88.0 -5.45393850338 -0.0352387170203
90 89.0 -5.41865505462 -0.0353131070729
91 90.0 -5.38334233438 -0.0352973681855
92 91.0 -5.34809011465 -0.0351922465446
93 92.0 -5.31298732458 -0.0349986814067
94 93.0 -5.27812185824 -0.034717803342
95 94.0 -5.24358038438 -0.0343509320285
96 95.0 -5.2094481586 -0.0338995736008
97 96.0 -5.17580883839 -0.0333654175598
98 97.0 -5.14274430152 -0.0327503332496
99 98.0 -5.11033446814 -0.0320563659092
100 99.0 -5.07865712698 -0.0312857323082
101 100.0 -5.04778776623 -0.0304408159764
102 101.0 -5.01779940929 -0.0295241620384
103 102.0 -4.98876245596 -0.0285384716647
104 103.0 -4.96074452928 -0.0274865961525
105 104.0 -4.93381032851 -0.0263715306507
106 105.0 -4.90802148862 -0.0251964075427
107 106.0 -4.88343644644 -0.0239644895038
108 107.0 -4.86011031397 -0.0226791622487
109 108.0 -4.83809475914 -0.0213439269874
110 109.0 -4.81743789414 -0.0199623926068
111 110.0 -4.79818417182 -0.0185382675969
112 111.0 -4.78037429015 -0.0170753517415
113 112.0 -4.76404510526 -0.0155775275918
114 113.0 -4.74922955293 -0.0140487517461
115 114.0 -4.73595657904 -0.0124930459538
116 115.0 -4.7242510789 -0.0109144880672
117 116.0 -4.71413384576 -0.00931720286182
118 117.0 -4.70562152846 -0.00770535274772
119 118.0 -4.69872659855 -0.00608312839491
120 119.0 -4.69345732669 -0.00445473929448
121 120.0 -4.6898177686 -0.00282440427898
122 121.0 -4.68780776044 -0.00119634202478
123 122.0 -4.68742292374 0.000425238440527
124 123.0 -4.68865467977 0.0020361472029
125 124.0 -4.69149027336 0.00363222287571
126 125.0 -4.69591280613 0.00520934194008
127 126.0 -4.70190127895 0.0067634279891
128 127.0 -4.70943064365 0.00829046085365
129 128.0 -4.71847186379 0.00978648558781
130 129.0 -4.72899198423 0.0112476212922
131 130.0 -4.74095420961 0.0126700697544
132 131.0 -4.7543179912 0.0140501238848
133 132.0 -4.76903912216 0.0153841759291
134 133.0 -4.78506984093 0.0166687254364
135 134.0 -4.80235894235 0.0179003869651
136 135.0 -4.82085189642 0.0190758975074
137 136.0 -4.84049097437 0.0201921236154
138 137.0 -4.86121538156 0.0212460682116
139 138.0 -4.88296139722 0.0222348770682
140 139.0 -4.90566252032 0.0231558449399
141 140.0 -4.9292496215 0.0240064213355
142 141.0 -4.95365110055 0.0247842159162
143 142.0 -4.97879304911 0.0254870035063
144 143.0 -5.00459941816 0.0261127287073
145 144.0 -5.03099218995 0.0266595101027
146 145.0 -5.05789155387 0.0271256440463
147 146.0 -5.08521608601 0.0275096080241
148 147.0 -5.11288293171 0.0278100635833
149 148.0 -5.14080799097 0.0280258588231
150 149.0 -5.16890610603 0.0281560304409
151 150.0 -5.19709125082 0.0281998053314
152 151.0 -5.22527672173 0.0281566017347
153 152.0 -5.25337532941 0.0280260299338
154 153.0 -5.28129959092 0.0278078924984
155 154.0 -5.30896192196 0.0275021840788
156 155.0 -5.33627482866 0.0271090907491
157 156.0 -5.36315109852 0.0266289889046
158 157.0 -5.38950398994 0.026062443717
159 158.0 -5.41524742011 0.0254102071518
160 159.0 -5.44029615055 0.0246732155563
161 160.0 -5.46456597019 0.0238525868232
162 161.0 -5.48797387528 0.0229496171403
163 162.0 -5.51043824587 0.0219657773349
164 163.0 -5.53187901853 0.0209027088232
165 164.0 -5.55221785468 0.0197622191769
166 165.0 -5.57137830441 0.0185462773191
167 166.0 -5.58928596528 0.0172570083629
168 167.0 -5.60586863576 0.0158966881068
169 168.0 -5.62105646307 0.0144677372016
170 169.0 -5.63478208493 0.0129727150063
171 170.0 -5.64698076513 0.0114143131467
172 171.0 -5.65759052241 0.00979534879707
173 172.0 -5.66655225257 0.00811875770075
174 173.0 -5.67380984344 0.00638758694863
175 174.0 -5.67931028251 0.00460498753534
176 175.0 -5.68300375706 0.00277420671195
177 176.0 -5.68484374646 0.000898580155594
178 177.0 -5.68478710669 -0.00101847602368
179 178.0 -5.68279414663 -0.00297347341791
180 179.0 -5.67882869631 -0.00496285957718
181 180.0 -5.67285816674 -0.00698302636509
182 181.0 -5.6648536014 -0.00903031839234
183 182.0 -5.65478971926 -0.0111010415069
184 183.0 -5.64264494925 -0.0131914713189
185 184.0 -5.62840145627 -0.0152978617389
186 185.0 -5.6120451586 -0.017416453508
187 186.0 -5.59356573683 -0.0195434826976
188 187.0 -5.57295663425 -0.0216751891584
189 188.0 -5.55021504898 -0.0238078248974
190 189.0 -5.52534191754 -0.0259376623617
191 190.0 -5.4983418904 -0.0280610026087
192 191.0 -5.46922329932 -0.0301741833429
193 192.0 -5.43799811672 -0.0322735868002
194 193.0 -5.40468190731 -0.0343556474589
195 194.0 -5.36929377207 -0.0364168595607
196 195.0 -5.33185628476 -0.0384537844225
197 196.0 -5.29239542138 -0.0404630575223
198 197.0 -5.25094048245 -0.0424413953416
199 198.0 -5.20752400881 -0.0443856019501
200 199.0 -5.16218169074 -0.0462925753151
201 200.0 -5.11495227114 -0.0481593133234
202 201.0 -5.06587744261 -0.0499829195012
203 202.0 -5.01500173918 -0.0517606084187
204 203.0 -4.96237242264 -0.0534897107689
205 204.0 -4.90803936404 -0.055167678109
206 205.0 -4.85205492059 -0.0567920872546
207 206.0 -4.79447380837 -0.0583606443179
208 207.0 -4.73535297113 -0.0598711883816
209 208.0 -4.6747514457 -0.0613216948024
210 209.0 -4.61273022413 -0.0627102781377
211 210.0 -4.54935211328 -0.0640351946902
212 211.0 -4.4846815919 -0.0652948446678
213 212.0 -4.41878466581 -0.0664877739558
214 213.0 -4.35172872155 -0.0676126754981
215 214.0 -4.28358237872 -0.0686683902899
216 215.0 -4.21441534165 -0.0696539079796
217 216.0 -4.14429825061 -0.070568367083
218 217.0 -4.07330253293 -0.0714110548116
219 218.0 -4.00150025463 -0.0721814065199
220 219.0 -3.92896397266 -0.072879004774
221 220.0 -3.85576658834 -0.0735035780505
222 221.0 -3.78198120223 -0.0740549990687
223 222.0 -3.70768097086 -0.0745332827669
224 223.0 -3.63293896573 -0.0749385839297
225 224.0 -3.5578280347 -0.0752711944755
226 225.0 -3.48242066643 -0.075531540416
227 226.0 -3.4067888579 -0.0757201784978
228 227.0 -3.33100398548 -0.0758377925383
229 228.0 -3.25513667985 -0.0758851894693
230 229.0 -3.17925670492 -0.0758632951011
231 230.0 -3.10343284123 -0.0757731496217
232 231.0 -3.02773277394 -0.0756159028468
233 232.0 -2.95222298559 -0.0753928092342
234 233.0 -2.87696865416 -0.0751052226812
235 234.0 -2.80203355622 -0.0747545911191
236 235.0 -2.72747997572 -0.0743424509249
237 236.0 -2.65336861841 -0.073870421164
238 237.0 -2.57975853208 -0.0733401976859
239 238.0 -2.50670703279 -0.0727535470871
240 239.0 -2.4342696372 -0.0721123005638
241 240.0 -2.36250000104 -0.0714183476691
242 241.0 -2.29144986396 -0.0706736299971
243 242.0 -2.22116900065 -0.0698801348102
244 243.0 -2.15170517837 -0.0690398886302
245 244.0 -2.0831041209 -0.0681549508121
246 245.0 -2.01540947892 -0.067227407119
247 246.0 -1.94866280684 -0.0662593633171
248 247.0 -1.88290354594 -0.0652529388105
249 248.0 -1.81816901389 -0.0642102603325
250 249.0 -1.7544944006 -0.0631334557138
251 250.0 -1.69191277013 -0.0620246477436
252 251.0 -1.6304550688 -0.0608859481423
253 252.0 -1.57015013921 -0.059719451663
254 253.0 -1.51102474011 -0.0585272303374
255 254.0 -1.45310357187 -0.0573113278834
256 255.0 -1.39640930762 -0.0560737542899
257 256.0 -1.34096262951 -0.054816480593
258 257.0 -1.28678227024 -0.0535414338587
259 258.0 -1.23388505944 -0.0522504923856
260 259.0 -1.18228597475 -0.0509454811405
261 260.0 -1.13199819729 -0.0496281674395
262 261.0 -1.08303317143 -0.0483002568854
263 262.0 -1.03540066834 -0.046963389572
264 263.0 -0.989108853377 -0.0456191365664
265 264.0 -0.944164356669 -0.0442689966762
266 265.0 -0.900572346917 -0.0429143935113
267 266.0 -0.858336607922 -0.0415566728462
268 267.0 -0.817459617608 -0.0401971002897
269 268.0 -0.777942629232 -0.0388368592669
270 269.0 -0.739785754436 -0.0374770493178
271 270.0 -0.702988047855 -0.0361186847156
272 271.0 -0.667547592939 -0.0347626934072
273 272.0 -0.633461588675 -0.0334099162773
274 273.0 -0.600726436882 -0.0320611067354
275 274.0 -0.569337829756 -0.0307169306269
276 275.0 -0.539290837348 -0.0293779664649
277 276.0 -0.510579994645 -0.0280447059807
278 277.0 -0.483199387947 -0.0267175549897
279 278.0 -0.457142740217 -0.0253968345674
280 279.0 -0.432403495111 -0.0240827825309
281 280.0 -0.408974899365 -0.0227755552188
282 281.0 -0.386850083265 -0.0214752295619
283 282.0 -0.366022138902 -0.020181805438
284 283.0 -0.346484195932 -0.0188952082997
285 284.0 -0.328229494574 -0.0176152920667
286 285.0 -0.311251455597 -0.0163418422722
287 286.0 -0.295543747024 -0.0150745794496
288 287.0 -0.28110034735 -0.0138131627512
289 288.0 -0.267915605017 -0.0125571937823
290 289.0 -0.255984293962 -0.011306220639
291 290.0 -0.245301665026 -0.0100597421363
292 291.0 -0.235863493049 -0.00881721220956
293 292.0 -0.22766611948 -0.00757804447631
294 293.0 -0.220706490355 -0.00634161694135
295 294.0 -0.214982189503 -0.00510727682957
296 295.0 -0.210491466861 -0.00387434552992
297 296.0 -0.207233261801 -0.00264212363344
298 297.0 -0.205207221373 -0.00140989604849
299 298.0 -0.204413713408 -0.00017693717569
300 299.0 -0.204853834414 0.0010574838751
301 300.0 -0.206529412255 0.00229409804323
302 301.0 -0.209443003569 0.00353363106913
303 302.0 -0.213597885954 0.00477679825726
304 303.0 -0.218998044922 0.00602429926791
305 304.0 -0.22564815567 0.00727681295572
306 305.0 -0.23355355972 0.00853499227222
307 306.0 -0.2427202365 0.00979945924997
308 307.0 -0.253154769958 0.0110708000854
309 308.0 -0.264864310313 0.0123495603372
310 309.0 -0.277856531075 0.0136362402565
311 310.0 -0.292139581459 0.0149312902659
312 311.0 -0.307722034364 0.0162351066015
313 312.0 -0.324612830087 0.0175480271349
314 313.0 -0.342821215943 0.0188703273888
315 314.0 -0.362356682012 0.0202022167596
316 315.0 -0.383228893218 0.0215438349636
317 316.0 -0.405447617967 0.0228952487148
318 317.0 -0.429022653586 0.0242564486517
319 318.0 -0.45396374882 0.0256273465206
320 319.0 -0.480280523637 0.0270077726275
321 320.0 -0.507982386639 0.0283974735696
322 321.0 -0.537078450328 0.029796110253
323 322.0 -0.567577444555 0.0312032562068
324 323.0 -0.59948762842 0.0326183962009
325 324.0 -0.632816700956 0.0340409251716
326 325.0 -0.667571710883 0.0354701474639
327 326.0 -0.703758965776 0.0369052763923
328 327.0 -0.741383940946 0.038345434125
329 328.0 -0.780451188376 0.0397896518935
330 329.0 -0.820964246018 0.0412368705304
331 330.0 -0.862925547807 0.042685941334
332 331.0 -0.906336334692 0.0441356272615
333 332.0 -0.951196567028 0.045584604448
334 333.0 -0.997504838648 0.0470314640498
335 334.0 -1.04525829294 0.048474714408
336 335.0 -1.09445254125 0.0499127835288
337 336.0 -1.1450815839 0.0513440218749
338 337.0 -1.1971377342 0.0527667054614
339 338.0 -1.25061154564 0.0541790392498
340 339.0 -1.30549174267 0.0555791608316
341 340.0 -1.36176515529 0.0569651443923
342 341.0 -1.41941665773 0.0583350049463
343 342.0 -1.47842911151 0.0596867028317
344 343.0 -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 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
11 10.0 -3.30856942003 0.0758590850738
12 11.0 -3.38438599377 0.0757623292865
13 12.0 -3.46007047791 0.0755947754951
14 13.0 -3.53555170381 0.0753557030426
15 14.0 -3.61075784476 0.0750445172025
16 15.0 -3.68561654392 0.0746607529305
17 16.0 -3.76005504566 0.0742040783151
18 17.0 -3.83400033034 0.0736742977129
19 18.0 -3.907379252 0.0730713545594
20 19.0 -3.98011867868 0.0723953338429
21 20.0 -4.0521456351 0.0716464642332
22 21.0 -4.12338744726 0.0708251198546
23 22.0 -4.19377188857 0.0699318216967
24 23.0 -4.26322732737 0.0689672386556
25 24.0 -4.33168287509 0.0679321881993
26 25.0 -4.39906853508 0.0668276366524
27 26.0 -4.46531535141 0.0656546990963
28 27.0 -4.53035555742 0.0644146388823
29 28.0 -4.59412272358 0.0631088667546
30 29.0 -4.65655190431 0.061738939584
31 30.0 -4.71757978327 0.0603065587109
32 31.0 -4.77714481686 0.0588135679005
33 32.0 -4.83518737548 0.057261950911
34 33.0 -4.89164988211 0.0556538286799
35 34.0 -4.94647694795 0.0539914561312
36 35.0 -4.99961550465 0.0522772186102
37 36.0 -5.05101493277 0.0505136279528
38 37.0 -5.10062718621 0.048703318195
39 38.0 -5.14840691207 0.0468490409338
40 39.0 -5.19431156578 0.0449536603471
41 40.0 -5.23830152101 0.0430201478838
42 41.0 -5.28034017422 0.0410515766363
43 42.0 -5.3203940433 0.0390511154063
44 43.0 -5.35843286021 0.0370220224793
45 44.0 -5.39442965726 0.0349676391193
46 45.0 -5.4283608467 0.0328913828015
47 46.0 -5.46020629342 0.0307967401964
48 47.0 -5.48994938059 0.028687259923
49 48.0 -5.51757706789 0.0265665450883
50 49.0 -5.54307994213 0.0244382456298
51 50.0 -5.56645226024 0.0223060504811
52 51.0 -5.58769198425 0.0201736795783
53 52.0 -5.60680080825 0.0180448757265
54 53.0 -5.62378417713 0.0159233963481
55 54.0 -5.63865129702 0.0138130051308
56 55.0 -5.6514151374 0.0117174635982
57 56.0 -5.66209242462 0.00964052262251
58 57.0 -5.67070362704 0.00758591390103
59 58.0 -5.67727293157 0.00555734141841
60 59.0 -5.6818282117 0.00355847291538
61 60.0 -5.68440098698 0.00159293138608
62 61.0 -5.68502637408 -0.000335713374531
63 62.0 -5.68374302934 -0.00222395315148
64 63.0 -5.68059308309 -0.0040683495974
65 64.0 -5.67562206565 -0.00586554240548
66 65.0 -5.66887882528 -0.00761225734683
67 66.0 -5.66041543813 -0.00930531415106
68 67.0 -5.65028711044 -0.0109416342099
69 68.0 -5.63855207307 -0.0125182480831
70 69.0 -5.6252714687 -0.0140323027883
71 70.0 -5.61050923182 -0.0154810688529
72 71.0 -5.59433196178 -0.0168619471125
73 72.0 -5.57680878923 -0.0181724752358
74 73.0 -5.5580112361 -0.019410333958
75 74.0 -5.53801306959 -0.0205733530082
76 75.0 -5.51689015031 -0.0216595167121
77 76.0 -5.49472027505 -0.0226669692568
78 77.0 -5.47158301441 -0.0235940196022
79 78.0 -5.44755954575 -0.0244391460249
80 79.0 -5.42273248172 -0.0252010002837
81 80.0 -5.3971856949 -0.0258784113929
82 81.0 -5.37100413881 -0.0264703889936
83 82.0 -5.34427366574 -0.0269761263135
84 83.0 -5.31708084192 -0.0273950027051
85 84.0 -5.28951276022 -0.0277265857564
86 85.0 -5.26165685114 -0.0279706329651
87 86.0 -5.23360069216 -0.0281270929735
88 87.0 -5.20543181621 -0.0281961063563
89 88.0 -5.17723751951 -0.0281780059613
90 89.0 -5.14910466934 -0.0280733167983
91 90.0 -5.12111951208 -0.0278827554757
92 91.0 -5.09336748214 -0.0276072291861
93 92.0 -5.06593301201 -0.0272478342399
94 93.0 -5.0388993441 -0.026805854151
95 94.0 -5.01234834466 -0.0262827572773
96 95.0 -4.98636032033 -0.0256801940208
97 96.0 -4.96101383762 -0.0249999935924
98 97.0 -4.93638554598 -0.0242441603499
99 98.0 -4.91255000457 -0.0234148697145
100 99.0 -4.88957951348 -0.0225144636776
101 100.0 -4.86754394953 -0.0215454459053
102 101.0 -4.84651060724 -0.0205104764546
103 102.0 -4.8265440452 -0.01941236611
104 103.0 -4.80770593836 -0.0182540703564
105 104.0 -4.79005493648 -0.0170386830008
106 105.0 -4.77364652914 -0.0157694294583
107 106.0 -4.7585329176 -0.0144496597171
108 107.0 -4.74476289391 -0.0130828410011
109 108.0 -4.73238172744 -0.0116725501446
110 109.0 -4.72143105919 -0.0102224657007
111 110.0 -4.71194880414 -0.00873635979846
112 111.0 -4.70396906182 -0.0072180897712
113 112.0 -4.69752203541 -0.00567158957449
114 113.0 -4.69263395945 -0.00410086101469
115 114.0 -4.68932703648 -0.00250996480925
116 115.0 -4.68761938265 -0.000903011500147
117 116.0 -4.68752498248 0.00071584775762
118 117.0 -4.68905365291 0.00234243051027
119 118.0 -4.69221101668 0.00397253239976
120 119.0 -4.69699848518 0.00560193661579
121 120.0 -4.70341325069 0.00722642338265
122 121.0 -4.71144828821 0.00884177945771
123 122.0 -4.72109236669 0.0104438076188
124 123.0 -4.73233006984 0.0120283361174
125 124.0 -4.74514182625 0.0135912280748
126 125.0 -4.75950394898 0.0151283907985
127 126.0 -4.77538868431 0.0166357849963
128 127.0 -4.79276426974 0.0181094338658
129 128.0 -4.81159500092 0.0195454320375
130 129.0 -4.83184130754 0.0209399543498
131 130.0 -4.8534598378 0.0222892644342
132 131.0 -4.87640355143 0.0235897230915
133 132.0 -4.90062182095 0.0248377964369
134 133.0 -4.92606054096 0.0260300637961
135 134.0 -4.95266224518 0.0271632253326
136 135.0 -4.98036623096 0.028234109388
137 136.0 -5.00910869107 0.0292396795182
138 137.0 -5.03882285221 0.0301770412082
139 138.0 -5.06943912022 0.0310434482505
140 139.0 -5.10088523142 0.0318363087705
141 140.0 -5.13308640979 0.0325531908865
142 141.0 -5.16596552963 0.0331918279898
143 142.0 -5.19944328334 0.0337501236332
144 143.0 -5.23343835383 0.0342261560164
145 144.0 -5.26786759123 0.0346181820585
146 145.0 -5.30264619353 0.0349246410472
147 146.0 -5.33768789051 0.0351441578585
148 147.0 -5.37290513082 0.0352755457383
149 148.0 -5.40820927152 0.0353178086401
150 149.0 -5.4435107698 0.0352701431151
151 150.0 -5.4787193763 0.0351319397498
152 151.0 -5.51374432971 0.0349027841491
153 152.0 -5.54849455206 0.0345824574643
154 153.0 -5.58287884436 0.0341709364636
155 154.0 -5.61680608206 0.0336683931487
156 155.0 -5.65018540988 0.0330751939177
157 156.0 -5.68292643563 0.0323918982779
158 157.0 -5.71493942249 0.0316192571138
159 158.0 -5.74613547931 0.0307582105139
160 159.0 -5.77642674856 0.029809885165
161 160.0 -5.80572659147 0.0287755913197
162 161.0 -5.83394976986 0.0276568193473
163 162.0 -5.86101262442 0.0264552358763
164 163.0 -5.8868332488 0.025172679541
165 164.0 -5.91133165941 0.0238111563427
166 165.0 -5.93442996024 0.0223728346376
167 166.0 -5.95605250261 0.0208600397671
168 167.0 -5.97612603931 0.0192752483425
169 168.0 -5.99457987285 0.0176210822011
170 169.0 -6.01134599757 0.015900302049
171 170.0 -6.02635923519 0.014115800807
172 171.0 -6.03955736358 0.0122705966784
173 172.0 -6.05088123845 0.0103678259555
174 173.0 -6.0602749078 0.00841073558436
175 174.0 -6.06768571866 0.00640267550713
176 175.0 -6.0730644163 0.00434709080102
177 176.0 -6.07636523524 0.00224751363529
178 177.0 -6.07754598232 0.000107555066143
179 178.0 -6.07656811141 -0.00206910330914
180 179.0 -6.07339678973 -0.00427871781763
181 180.0 -6.06800095563 -0.00651749127408
182 181.0 -6.06035336781 -0.00878158162059
183 182.0 -6.05043064586 -0.0110671106207
184 183.0 -6.03821330204 -0.0133701725859
185 184.0 -6.02368576439 -0.0156868431131
186 185.0 -6.00683639108 -0.0180131878107
187 186.0 -5.98765747603 -0.0203452709919
188 187.0 -5.96614524589 -0.0226791643135
189 188.0 -5.94229984843 -0.025010955339
190 189.0 -5.91612533236 -0.0273367560054
191 190.0 -5.88762961878 -0.0296527109716
192 191.0 -5.85682446433 -0.0319550058299
193 192.0 -5.82372541626 -0.0342398751598
194 193.0 -5.78835175943 -0.0365036104045
195 194.0 -5.75072645562 -0.0387425675516
196 195.0 -5.71087607524 -0.0409531746008
197 196.0 -5.66883072166 -0.0431319387984
198 197.0 -5.62462394846 -0.0452754536249
199 198.0 -5.57829266983 -0.0473804055171
200 199.0 -5.5298770643 -0.0494435803104
201 200.0 -5.47942047235 -0.0514618693867
202 201.0 -5.42696928781 -0.0534322755136
203 202.0 -5.37257284377 -0.055351918363
204 203.0 -5.316283293 -0.0572180396955
205 204.0 -5.25815548345 -0.059028008202
206 205.0 -5.19824682901 -0.0607793239895
207 206.0 -5.13661717604 -0.0624696227052
208 207.0 -5.0733286659 -0.0640966792879
209 208.0 -5.00844559393 -0.0656584113417
210 209.0 -4.94203426529 -0.0671528821253
211 210.0 -4.87416284794 -0.0685783031513
212 211.0 -4.80490122327 -0.0699330363936
213 212.0 -4.7343208347 -0.0712155960973
214 213.0 -4.66249453466 -0.0724246501921
215 214.0 -4.58949643037 -0.0735590213066
216 215.0 -4.51540172879 -0.0746176873849
217 216.0 -4.44028658118 -0.0755997819067
218 217.0 -4.3642279276 -0.0765045937139
219 218.0 -4.28730334182 -0.0773315664459
220 219.0 -4.20959087694 -0.0780802975905
221 220.0 -4.13116891218 -0.0787505371538
222 221.0 -4.0521160012 -0.0793421859574
223 222.0 -3.97251072229 -0.0798552935693
224 223.0 -3.89243153076 -0.0802900558785
225 224.0 -3.81195661404 -0.0806468123209
226 225.0 -3.73116374964 -0.0809260427693
227 226.0 -3.65013016636 -0.0811283640964
228 227.0 -3.56893240921 -0.0812545264246
229 228.0 -3.48764620813 -0.0813054090744
230 229.0 -3.4063463509 -0.0812820162266
231 230.0 -3.32510656064 -0.0811854723104
232 231.0 -3.24399937793 -0.081017017134
233 232.0 -3.16309604794 -0.0807780007742
234 233.0 -3.08246641287 -0.0804698782381
235 234.0 -3.00217880976 -0.0800942039176
236 235.0 -2.92229997393 -0.079652625851
237 236.0 -2.84289494829 -0.0791468798106
238 237.0 -2.76402699866 -0.0785787832348
239 238.0 -2.68575753514 -0.0779502290223
240 239.0 -2.60814603984 -0.077263179207
241 240.0 -2.53125000097 -0.0765196585342
242 241.0 -2.4551248533 -0.0757217479546
243 242.0 -2.37982392531 -0.0748715780578
244 243.0 -2.30539839282 -0.073971322463
245 244.0 -2.23189723927 -0.0730231911866
246 245.0 -2.15936722267 -0.072029424007
247 246.0 -2.0878528491 -0.0709922838436
248 247.0 -2.01739635293 -0.0699140501714
249 248.0 -1.94803768347 -0.0687970124882
250 249.0 -1.87981449824 -0.0676434638537
251 250.0 -1.81276216256 -0.0664556945194
252 251.0 -1.74691375554 -0.0652359856651
253 252.0 -1.68230008218 -0.0639866032624
254 253.0 -1.61894969164 -0.0627097920793
255 254.0 -1.55688890134 -0.0614077698443
256 255.0 -1.49614182687 -0.0600827215855
257 256.0 -1.43673041741 -0.05873679416
258 257.0 -1.37867449659 -0.0573720909874
259 258.0 -1.32199180845 -0.0559906670036
260 259.0 -1.26669806833 -0.0545945238457
261 260.0 -1.21280701853 -0.0531856052829
262 261.0 -1.1603304883 -0.0517657929031
263 262.0 -1.1092784581 -0.0503369020679
264 263.0 -1.05965912771 -0.0489006781451
265 264.0 -1.01147898802 -0.0474587930279
266 265.0 -0.964742896092 -0.0460128419505
267 266.0 -0.919454153297 -0.0445643406057
268 267.0 -0.875614586172 -0.0431147225719
269 268.0 -0.833224629688 -0.0416653370554
270 269.0 -0.792283412613 -0.0402174469521
271 270.0 -0.752788844664 -0.038772227232
272 271.0 -0.714737705101 -0.0373307636499
273 272.0 -0.67812573245 -0.0358940517831
274 273.0 -0.642947715028 -0.0344629963972
275 274.0 -0.609197581934 -0.0330384111393
276 275.0 -0.576868494182 -0.0316210185584
277 276.0 -0.545952935658 -0.0302114504483
278 277.0 -0.51644280357 -0.0288102485125
279 278.0 -0.488329498068 -0.0274178653447
280 279.0 -0.461604010741 -0.0260346657211
281 280.0 -0.436257011655 -0.0246609281969
282 281.0 -0.412278934657 -0.023296847002
283 282.0 -0.389660060626 -0.0219425342253
284 283.0 -0.368390598407 -0.0205980222818
285 284.0 -0.348460763137 -0.01926326665
286 285.0 -0.329860851704 -0.0179381488715
287 286.0 -0.312581315078 -0.0166224797996
288 287.0 -0.296612827279 -0.015316003087
289 288.0 -0.281946350734 -0.0140183988977
290 289.0 -0.268573197826 -0.0127292878319
291 290.0 -0.256485088408 -0.0114482350481
292 291.0 -0.245674203109 -0.0101747545698
293 292.0 -0.236133232246 -0.00890831375923
294 293.0 -0.227855420178 -0.00764833794542
295 294.0 -0.220834604976 -0.00639421518813
296 295.0 -0.215065253253 -0.00514530116277
297 296.0 -0.210542490065 -0.00390092414876
298 297.0 -0.207262123775 -0.00266039010467
299 298.0 -0.205220665805 -0.00142298781263
300 299.0 -0.204415345223 -0.000187994074493
301 300.0 -0.204844118104 0.00104532105779
302 301.0 -0.206505671662 0.00227768903543
303 302.0 -0.209399423126 0.0035098375675
304 303.0 -0.213525513386 0.00474248539479
305 304.0 -0.218884795423 0.00597633710062
306 305.0 -0.225478817581 0.00721207797616
307 306.0 -0.233309801737 0.00845036895769
308 307.0 -0.242380616448 0.00969184165314
309 308.0 -0.252694745185 0.0109370934746
310 309.0 -0.264256249747 0.0121866828936
311 310.0 -0.277069729013 0.0134411248358
312 311.0 -0.291140273151 0.0147008862297
313 312.0 -0.306473413467 0.0159663817261
314 313.0 -0.323075068066 0.0172379696031
315 314.0 -0.340951483513 0.018515947869
316 315.0 -0.360109172702 0.0198005505798
317 316.0 -0.380554849155 0.0210919443819
318 317.0 -0.402295357987 0.0223902252933
319 318.0 -0.425337603767 0.0236954157356
320 319.0 -0.449688475549 0.0250074618263
321 320.0 -0.475354769327 0.0263262309427
322 321.0 -0.50234310819 0.0276515095659
323 322.0 -0.530659860472 0.0289830014145
324 323.0 -0.560311056174 0.0303203258736
325 324.0 -0.59130230198 0.0316630167284
326 325.0 -0.623638695141 0.0330105212056
327 326.0 -0.657324736579 0.0343621993296
328 327.0 -0.692364243488 0.0357173235955
329 328.0 -0.728760261774 0.0370750789637
330 329.0 -0.766514978659 0.0384345631765
331 330.0 -0.805629635748 0.0397947873984
332 331.0 -0.846104442913 0.04115467718
333 332.0 -0.887938493289 0.042513073745
334 333.0 -0.93112967973 0.0438687355968
335 334.0 -0.975674613021 0.0452203404434
336 335.0 -1.02156854218 0.0465664874361
337 336.0 -1.06880527714 0.0479056997168
338 337.0 -1.11737711415 0.0492364272675
339 338.0 -1.16727476416 0.0505570500574
340 339.0 -1.2184872845 0.051865881477
341 340.0 -1.27100201415 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

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# -- 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

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# -- 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

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# 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

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# 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

24
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# 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 ../

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------- 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.)

476
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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 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 2 2 0.000000 1.0000 0
29 2 1 1 0.000000 1.0000 0
30 2 2 2 0.000000 1.0000 0
31 2 1 1 0.000000 1.0000 0
32 2 2 2 0.000000 1.0000 0
33 2 1 1 0.000000 1.0000 0
34 2 3 3 0.000000 1.0000 0
35 2 3 3 0.000000 1.0000 0
36 2 1 1 0.000000 1.0000 0
37 2 2 2 0.000000 1.0000 0
38 2 1 1 0.000000 1.0000 0
39 2 2 2 0.000000 1.0000 0
40 2 1 1 0.000000 1.0000 0
41 2 2 2 0.000000 1.0000 0
42 2 3 3 0.000000 1.0000 0
43 2 3 3 0.000000 1.0000 0
44 2 3 3 0.000000 1.0000 0
45 2 1 1 0.000000 1.0000 0
46 2 1 1 0.000000 1.0000 0
47 2 2 2 0.000000 1.0000 0
48 2 2 2 0.000000 1.0000 0
49 2 1 1 0.000000 1.0000 0
50 2 1 1 0.000000 1.0000 0
51 2 2 2 0.000000 1.0000 0
52 2 2 2 0.000000 1.0000 0
53 2 1 1 0.000000 1.0000 0
54 2 2 2 0.000000 1.0000 0
55 3 2 2 0.000000 1.0000 0
56 3 1 1 0.000000 1.0000 0
57 3 2 2 0.000000 1.0000 0
58 3 1 1 0.000000 1.0000 0
59 3 2 2 0.000000 1.0000 0
60 3 1 1 0.000000 1.0000 0
61 3 3 3 0.000000 1.0000 0
62 3 3 3 0.000000 1.0000 0
63 3 1 1 0.000000 1.0000 0
64 3 2 2 0.000000 1.0000 0
65 3 1 1 0.000000 1.0000 0
66 3 2 2 0.000000 1.0000 0
67 3 1 1 0.000000 1.0000 0
68 3 2 2 0.000000 1.0000 0
69 3 3 3 0.000000 1.0000 0
70 3 3 3 0.000000 1.0000 0
71 3 3 3 0.000000 1.0000 0
72 3 1 1 0.000000 1.0000 0
73 3 1 1 0.000000 1.0000 0
74 3 2 2 0.000000 1.0000 0
75 3 2 2 0.000000 1.0000 0
76 3 1 1 0.000000 1.0000 0
77 3 1 1 0.000000 1.0000 0
78 3 2 2 0.000000 1.0000 0
79 3 2 2 0.000000 1.0000 0
80 3 1 1 0.000000 1.0000 0
81 3 2 2 0.000000 1.0000 0
82 4 2 2 0.000000 1.0000 0
83 4 1 1 0.000000 1.0000 0
84 4 2 2 0.000000 1.0000 0
85 4 1 1 0.000000 1.0000 0
86 4 2 2 0.000000 1.0000 0
87 4 1 1 0.000000 1.0000 0
88 4 3 3 0.000000 1.0000 0
89 4 3 3 0.000000 1.0000 0
90 4 1 1 0.000000 1.0000 0
91 4 2 2 0.000000 1.0000 0
92 4 1 1 0.000000 1.0000 0
93 4 2 2 0.000000 1.0000 0
94 4 1 1 0.000000 1.0000 0
95 4 2 2 0.000000 1.0000 0
96 4 3 3 0.000000 1.0000 0
97 4 3 3 0.000000 1.0000 0
98 4 3 3 0.000000 1.0000 0
99 4 1 1 0.000000 1.0000 0
100 4 1 1 0.000000 1.0000 0
101 4 2 2 0.000000 1.0000 0
102 4 2 2 0.000000 1.0000 0
103 4 1 1 0.000000 1.0000 0
104 4 1 1 0.000000 1.0000 0
105 4 2 2 0.000000 1.0000 0
106 4 2 2 0.000000 1.0000 0
107 4 1 1 0.000000 1.0000 0
108 4 2 2 0.000000 1.0000 0
109 5 2 2 0.000000 1.0000 0
110 5 1 1 0.000000 1.0000 0
111 5 2 2 0.000000 1.0000 0
112 5 1 1 0.000000 1.0000 0
113 5 2 2 0.000000 1.0000 0
114 5 1 1 0.000000 1.0000 0
115 5 3 3 0.000000 1.0000 0
116 5 3 3 0.000000 1.0000 0
117 5 1 1 0.000000 1.0000 0
118 5 2 2 0.000000 1.0000 0
119 5 1 1 0.000000 1.0000 0
120 5 2 2 0.000000 1.0000 0
121 5 1 1 0.000000 1.0000 0
122 5 2 2 0.000000 1.0000 0
123 5 3 3 0.000000 1.0000 0
124 5 3 3 0.000000 1.0000 0
125 5 3 3 0.000000 1.0000 0
126 5 1 1 0.000000 1.0000 0
127 5 1 1 0.000000 1.0000 0
128 5 2 2 0.000000 1.0000 0
129 5 2 2 0.000000 1.0000 0
130 5 1 1 0.000000 1.0000 0
131 5 1 1 0.000000 1.0000 0
132 5 2 2 0.000000 1.0000 0
133 5 2 2 0.000000 1.0000 0
134 5 1 1 0.000000 1.0000 0
135 5 2 2 0.000000 1.0000 0
136 6 2 2 0.000000 1.0000 0
137 6 1 1 0.000000 1.0000 0
138 6 2 2 0.000000 1.0000 0
139 6 1 1 0.000000 1.0000 0
140 6 2 2 0.000000 1.0000 0
141 6 1 1 0.000000 1.0000 0
142 6 3 3 0.000000 1.0000 0
143 6 3 3 0.000000 1.0000 0
144 6 1 1 0.000000 1.0000 0
145 6 2 2 0.000000 1.0000 0
146 6 1 1 0.000000 1.0000 0
147 6 2 2 0.000000 1.0000 0
148 6 1 1 0.000000 1.0000 0
149 6 2 2 0.000000 1.0000 0
150 6 3 3 0.000000 1.0000 0
151 6 3 3 0.000000 1.0000 0
152 6 3 3 0.000000 1.0000 0
153 6 1 1 0.000000 1.0000 0
154 6 1 1 0.000000 1.0000 0
155 6 2 2 0.000000 1.0000 0
156 6 2 2 0.000000 1.0000 0
157 6 1 1 0.000000 1.0000 0
158 6 1 1 0.000000 1.0000 0
159 6 2 2 0.000000 1.0000 0
160 6 2 2 0.000000 1.0000 0
161 6 1 1 0.000000 1.0000 0
162 6 2 2 0.000000 1.0000 0
163 7 2 2 0.000000 1.0000 0
164 7 1 1 0.000000 1.0000 0
165 7 2 2 0.000000 1.0000 0
166 7 1 1 0.000000 1.0000 0
167 7 2 2 0.000000 1.0000 0
168 7 1 1 0.000000 1.0000 0
169 7 3 3 0.000000 1.0000 0
170 7 3 3 0.000000 1.0000 0
171 7 1 1 0.000000 1.0000 0
172 7 2 2 0.000000 1.0000 0
173 7 1 1 0.000000 1.0000 0
174 7 2 2 0.000000 1.0000 0
175 7 1 1 0.000000 1.0000 0
176 7 2 2 0.000000 1.0000 0
177 7 3 3 0.000000 1.0000 0
178 7 3 3 0.000000 1.0000 0
179 7 3 3 0.000000 1.0000 0
180 7 1 1 0.000000 1.0000 0
181 7 1 1 0.000000 1.0000 0
182 7 2 2 0.000000 1.0000 0
183 7 2 2 0.000000 1.0000 0
184 7 1 1 0.000000 1.0000 0
185 7 1 1 0.000000 1.0000 0
186 7 2 2 0.000000 1.0000 0
187 7 2 2 0.000000 1.0000 0
188 7 1 1 0.000000 1.0000 0
189 7 2 2 0.000000 1.0000 0
190 8 2 2 0.000000 1.0000 0
191 8 1 1 0.000000 1.0000 0
192 8 2 2 0.000000 1.0000 0
193 8 1 1 0.000000 1.0000 0
194 8 2 2 0.000000 1.0000 0
195 8 1 1 0.000000 1.0000 0
196 8 3 3 0.000000 1.0000 0
197 8 3 3 0.000000 1.0000 0
198 8 1 1 0.000000 1.0000 0
199 8 2 2 0.000000 1.0000 0
200 8 1 1 0.000000 1.0000 0
201 8 2 2 0.000000 1.0000 0
202 8 1 1 0.000000 1.0000 0
203 8 2 2 0.000000 1.0000 0
204 8 3 3 0.000000 1.0000 0
205 8 3 3 0.000000 1.0000 0
206 8 3 3 0.000000 1.0000 0
207 8 1 1 0.000000 1.0000 0
208 8 1 1 0.000000 1.0000 0
209 8 2 2 0.000000 1.0000 0
210 8 2 2 0.000000 1.0000 0
211 8 1 1 0.000000 1.0000 0
212 8 1 1 0.000000 1.0000 0
213 8 2 2 0.000000 1.0000 0
214 8 2 2 0.000000 1.0000 0
215 8 1 1 0.000000 1.0000 0
216 8 2 2 0.000000 1.0000 0
217 9 4 4 0.000000 100.0000 0
218 10 4 4 0.000000 100.0000 0
219 11 4 4 0.000000 100.0000 0
220 12 4 4 0.000000 100.0000 0
221 13 4 4 0.000000 100.0000 0
222 14 4 4 0.000000 100.0000 0
223 15 4 4 0.000000 100.0000 0
224 16 4 4 0.000000 100.0000 0
208 !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 28 29 29 30
30 31 31 32 32 33 33 34
34 35 35 36 36 37 37 38
38 39 39 40 40 41 41 42
42 43 43 44 44 45 45 46
46 47 47 48 48 49 49 50
50 51 51 52 52 53 53 54
55 56 56 57 57 58 58 59
59 60 60 61 61 62 62 63
63 64 64 65 65 66 66 67
67 68 68 69 69 70 70 71
71 72 72 73 73 74 74 75
75 76 76 77 77 78 78 79
79 80 80 81 82 83 83 84
84 85 85 86 86 87 87 88
88 89 89 90 90 91 91 92
92 93 93 94 94 95 95 96
96 97 97 98 98 99 99 100
100 101 101 102 102 103 103 104
104 105 105 106 106 107 107 108
109 110 110 111 111 112 112 113
113 114 114 115 115 116 116 117
117 118 118 119 119 120 120 121
121 122 122 123 123 124 124 125
125 126 126 127 127 128 128 129
129 130 130 131 131 132 132 133
133 134 134 135 136 137 137 138
138 139 139 140 140 141 141 142
142 143 143 144 144 145 145 146
146 147 147 148 148 149 149 150
150 151 151 152 152 153 153 154
154 155 155 156 156 157 157 158
158 159 159 160 160 161 161 162
163 164 164 165 165 166 166 167
167 168 168 169 169 170 170 171
171 172 172 173 173 174 174 175
175 176 176 177 177 178 178 179
179 180 180 181 181 182 182 183
183 184 184 185 185 186 186 187
187 188 188 189 190 191 191 192
192 193 193 194 194 195 195 196
196 197 197 198 198 199 199 200
200 201 201 202 202 203 203 204
204 205 205 206 206 207 207 208
208 209 209 210 210 211 211 212
212 213 213 214 214 215 215 216
200 !NTHETA: angles
13 14 15 40 41 42 67 68 69
94 95 96 121 122 123 148 149 150
175 176 177 202 203 204 7 8 9
6 7 8 16 17 18 34 35 36
33 34 35 43 44 45 61 62 63
60 61 62 70 71 72 88 89 90
87 88 89 97 98 99 115 116 117
114 115 116 124 125 126 142 143 144
141 142 143 151 152 153 169 170 171
168 169 170 178 179 180 196 197 198
195 196 197 205 206 207 15 16 17
42 43 44 69 70 71 96 97 98
123 124 125 150 151 152 177 178 179
204 205 206 2 3 4 4 5 6
9 10 11 11 12 13 29 30 31
31 32 33 36 37 38 38 39 40
56 57 58 58 59 60 63 64 65
65 66 67 83 84 85 85 86 87
90 91 92 92 93 94 110 111 112
112 113 114 117 118 119 119 120 121
137 138 139 139 140 141 144 145 146
146 147 148 164 165 166 166 167 168
171 172 173 173 174 175 191 192 193
193 194 195 198 199 200 200 201 202
14 15 16 41 42 43 68 69 70
95 96 97 122 123 124 149 150 151
176 177 178 203 204 205 1 2 3
3 4 5 10 11 12 12 13 14
25 26 27 28 29 30 30 31 32
37 38 39 39 40 41 52 53 54
55 56 57 57 58 59 64 65 66
66 67 68 79 80 81 82 83 84
84 85 86 91 92 93 93 94 95
106 107 108 109 110 111 111 112 113
118 119 120 120 121 122 133 134 135
136 137 138 138 139 140 145 146 147
147 148 149 160 161 162 163 164 165
165 166 167 172 173 174 174 175 176
187 188 189 190 191 192 192 193 194
199 200 201 201 202 203 214 215 216
5 6 7 8 9 10 32 33 34
35 36 37 59 60 61 62 63 64
86 87 88 89 90 91 113 114 115
116 117 118 140 141 142 143 144 145
167 168 169 170 171 172 194 195 196
197 198 199 17 18 19 44 45 46
71 72 73 98 99 100 125 126 127
152 153 154 179 180 181 206 207 208
18 19 20 22 23 24 21 22 23
45 46 47 49 50 51 48 49 50
72 73 74 76 77 78 75 76 77
99 100 101 103 104 105 102 103 104
126 127 128 130 131 132 129 130 131
153 154 155 157 158 159 156 157 158
180 181 182 184 185 186 183 184 185
207 208 209 211 212 213 210 211 212
19 20 21 20 21 22 23 24 25
24 25 26 46 47 48 47 48 49
50 51 52 51 52 53 73 74 75
74 75 76 77 78 79 78 79 80
100 101 102 101 102 103 104 105 106
105 106 107 127 128 129 128 129 130
131 132 133 132 133 134 154 155 156
155 156 157 158 159 160 159 160 161
181 182 183 182 183 184 185 186 187
186 187 188 208 209 210 209 210 211
212 213 214 213 214 215
152 !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 28 29 30 31
29 30 31 32 30 31 32 33
31 32 33 34 35 36 37 38
36 37 38 39 37 38 39 40
38 39 40 41 39 40 41 42
42 43 44 45 43 44 45 46
44 45 46 47 45 46 47 48
46 47 48 49 47 48 49 50
48 49 50 51 49 50 51 52
50 51 52 53 51 52 53 54
55 56 57 58 56 57 58 59
57 58 59 60 58 59 60 61
62 63 64 65 63 64 65 66
64 65 66 67 65 66 67 68
66 67 68 69 69 70 71 72
70 71 72 73 71 72 73 74
72 73 74 75 73 74 75 76
74 75 76 77 75 76 77 78
76 77 78 79 77 78 79 80
78 79 80 81 82 83 84 85
83 84 85 86 84 85 86 87
85 86 87 88 89 90 91 92
90 91 92 93 91 92 93 94
92 93 94 95 93 94 95 96
96 97 98 99 97 98 99 100
98 99 100 101 99 100 101 102
100 101 102 103 101 102 103 104
102 103 104 105 103 104 105 106
104 105 106 107 105 106 107 108
109 110 111 112 110 111 112 113
111 112 113 114 112 113 114 115
116 117 118 119 117 118 119 120
118 119 120 121 119 120 121 122
120 121 122 123 123 124 125 126
124 125 126 127 125 126 127 128
126 127 128 129 127 128 129 130
128 129 130 131 129 130 131 132
130 131 132 133 131 132 133 134
132 133 134 135 136 137 138 139
137 138 139 140 138 139 140 141
139 140 141 142 143 144 145 146
144 145 146 147 145 146 147 148
146 147 148 149 147 148 149 150
150 151 152 153 151 152 153 154
152 153 154 155 153 154 155 156
154 155 156 157 155 156 157 158
156 157 158 159 157 158 159 160
158 159 160 161 159 160 161 162
163 164 165 166 164 165 166 167
165 166 167 168 166 167 168 169
170 171 172 173 171 172 173 174
172 173 174 175 173 174 175 176
174 175 176 177 177 178 179 180
178 179 180 181 179 180 181 182
180 181 182 183 181 182 183 184
182 183 184 185 183 184 185 186
184 185 186 187 185 186 187 188
186 187 188 189 190 191 192 193
191 192 193 194 192 193 194 195
193 194 195 196 197 198 199 200
198 199 200 201 199 200 201 202
200 201 202 203 201 202 203 204
204 205 206 207 205 206 207 208
206 207 208 209 207 208 209 210
208 209 210 211 209 210 211 212
210 211 212 213 211 212 213 214
212 213 214 215 213 214 215 216
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 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

BIN
tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=0tau_LR.jpg
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tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=67500tau_LR.jpg
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tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated.lt
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# 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

85
tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated_variants.lt
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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

87
tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_chaperone_table.py
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#!/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))

67
tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_dihedral_table.py
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@ -1,67 +0,0 @@
#!/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))

41
tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/minichaperone.lt
View File

@ -1,41 +0,0 @@
# 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.

72
tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.lt
View File

@ -1,72 +0,0 @@
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)
}

735
tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_dihedral_frustrated.dat
View File

@ -1,735 +0,0 @@
# 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
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13 12.0 -3.70721728841 0.0809938639029
14 13.0 -3.78808936748 0.080737451911
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228 227.0 -3.33100398548 -0.0758377925383
229 228.0 -3.25513667985 -0.0758851894693
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231 230.0 -3.10343284123 -0.0757731496217
232 231.0 -3.02773277394 -0.0756159028468
233 232.0 -2.95222298559 -0.0753928092342
234 233.0 -2.87696865416 -0.0751052226812
235 234.0 -2.80203355622 -0.0747545911191
236 235.0 -2.72747997572 -0.0743424509249
237 236.0 -2.65336861841 -0.073870421164
238 237.0 -2.57975853208 -0.0733401976859
239 238.0 -2.50670703279 -0.0727535470871
240 239.0 -2.4342696372 -0.0721123005638
241 240.0 -2.36250000104 -0.0714183476691
242 241.0 -2.29144986396 -0.0706736299971
243 242.0 -2.22116900065 -0.0698801348102
244 243.0 -2.15170517837 -0.0690398886302
245 244.0 -2.0831041209 -0.0681549508121
246 245.0 -2.01540947892 -0.067227407119
247 246.0 -1.94866280684 -0.0662593633171
248 247.0 -1.88290354594 -0.0652529388105
249 248.0 -1.81816901389 -0.0642102603325
250 249.0 -1.7544944006 -0.0631334557138
251 250.0 -1.69191277013 -0.0620246477436
252 251.0 -1.6304550688 -0.0608859481423
253 252.0 -1.57015013921 -0.059719451663
254 253.0 -1.51102474011 -0.0585272303374
255 254.0 -1.45310357187 -0.0573113278834
256 255.0 -1.39640930762 -0.0560737542899
257 256.0 -1.34096262951 -0.054816480593
258 257.0 -1.28678227024 -0.0535414338587
259 258.0 -1.23388505944 -0.0522504923856
260 259.0 -1.18228597475 -0.0509454811405
261 260.0 -1.13199819729 -0.0496281674395
262 261.0 -1.08303317143 -0.0483002568854
263 262.0 -1.03540066834 -0.046963389572
264 263.0 -0.989108853377 -0.0456191365664
265 264.0 -0.944164356669 -0.0442689966762
266 265.0 -0.900572346917 -0.0429143935113
267 266.0 -0.858336607922 -0.0415566728462
268 267.0 -0.817459617608 -0.0401971002897
269 268.0 -0.777942629232 -0.0388368592669
270 269.0 -0.739785754436 -0.0374770493178
271 270.0 -0.702988047855 -0.0361186847156
272 271.0 -0.667547592939 -0.0347626934072
273 272.0 -0.633461588675 -0.0334099162773
274 273.0 -0.600726436882 -0.0320611067354
275 274.0 -0.569337829756 -0.0307169306269
276 275.0 -0.539290837348 -0.0293779664649
277 276.0 -0.510579994645 -0.0280447059807
278 277.0 -0.483199387947 -0.0267175549897
279 278.0 -0.457142740217 -0.0253968345674
280 279.0 -0.432403495111 -0.0240827825309
281 280.0 -0.408974899365 -0.0227755552188
282 281.0 -0.386850083265 -0.0214752295619
283 282.0 -0.366022138902 -0.020181805438
284 283.0 -0.346484195932 -0.0188952082997
285 284.0 -0.328229494574 -0.0176152920667
286 285.0 -0.311251455597 -0.0163418422722
287 286.0 -0.295543747024 -0.0150745794496
288 287.0 -0.28110034735 -0.0138131627512
289 288.0 -0.267915605017 -0.0125571937823
290 289.0 -0.255984293962 -0.011306220639
291 290.0 -0.245301665026 -0.0100597421363
292 291.0 -0.235863493049 -0.00881721220956
293 292.0 -0.22766611948 -0.00757804447631
294 293.0 -0.220706490355 -0.00634161694135
295 294.0 -0.214982189503 -0.00510727682957
296 295.0 -0.210491466861 -0.00387434552992
297 296.0 -0.207233261801 -0.00264212363344
298 297.0 -0.205207221373 -0.00140989604849
299 298.0 -0.204413713408 -0.00017693717569
300 299.0 -0.204853834414 0.0010574838751
301 300.0 -0.206529412255 0.00229409804323
302 301.0 -0.209443003569 0.00353363106913
303 302.0 -0.213597885954 0.00477679825726
304 303.0 -0.218998044922 0.00602429926791
305 304.0 -0.22564815567 0.00727681295572
306 305.0 -0.23355355972 0.00853499227222
307 306.0 -0.2427202365 0.00979945924997
308 307.0 -0.253154769958 0.0110708000854
309 308.0 -0.264864310313 0.0123495603372
310 309.0 -0.277856531075 0.0136362402565
311 310.0 -0.292139581459 0.0149312902659
312 311.0 -0.307722034364 0.0162351066015
313 312.0 -0.324612830087 0.0175480271349
314 313.0 -0.342821215943 0.0188703273888
315 314.0 -0.362356682012 0.0202022167596
316 315.0 -0.383228893218 0.0215438349636
317 316.0 -0.405447617967 0.0228952487148
318 317.0 -0.429022653586 0.0242564486517
319 318.0 -0.45396374882 0.0256273465206
320 319.0 -0.480280523637 0.0270077726275
321 320.0 -0.507982386639 0.0283974735696
322 321.0 -0.537078450328 0.029796110253
323 322.0 -0.567577444555 0.0312032562068
324 323.0 -0.59948762842 0.0326183962009
325 324.0 -0.632816700956 0.0340409251716
326 325.0 -0.667571710883 0.0354701474639
327 326.0 -0.703758965776 0.0369052763923
328 327.0 -0.741383940946 0.038345434125
329 328.0 -0.780451188376 0.0397896518935
330 329.0 -0.820964246018 0.0412368705304
331 330.0 -0.862925547807 0.042685941334
332 331.0 -0.906336334692 0.0441356272615
333 332.0 -0.951196567028 0.045584604448
334 333.0 -0.997504838648 0.0470314640498
335 334.0 -1.04525829294 0.048474714408
336 335.0 -1.09445254125 0.0499127835288
337 336.0 -1.1450815839 0.0513440218749
338 337.0 -1.1971377342 0.0527667054614
339 338.0 -1.25061154564 0.0541790392498
340 339.0 -1.30549174267 0.0555791608316
341 340.0 -1.36176515529 0.0569651443923
342 341.0 -1.41941665773 0.0583350049463
343 342.0 -1.47842911151 0.0596867028317
344 343.0 -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 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
11 10.0 -3.30856942003 0.0758590850738
12 11.0 -3.38438599377 0.0757623292865
13 12.0 -3.46007047791 0.0755947754951
14 13.0 -3.53555170381 0.0753557030426
15 14.0 -3.61075784476 0.0750445172025
16 15.0 -3.68561654392 0.0746607529305
17 16.0 -3.76005504566 0.0742040783151
18 17.0 -3.83400033034 0.0736742977129
19 18.0 -3.907379252 0.0730713545594
20 19.0 -3.98011867868 0.0723953338429
21 20.0 -4.0521456351 0.0716464642332
22 21.0 -4.12338744726 0.0708251198546
23 22.0 -4.19377188857 0.0699318216967
24 23.0 -4.26322732737 0.0689672386556
25 24.0 -4.33168287509 0.0679321881993
26 25.0 -4.39906853508 0.0668276366524
27 26.0 -4.46531535141 0.0656546990963
28 27.0 -4.53035555742 0.0644146388823
29 28.0 -4.59412272358 0.0631088667546
30 29.0 -4.65655190431 0.061738939584
31 30.0 -4.71757978327 0.0603065587109
32 31.0 -4.77714481686 0.0588135679005
33 32.0 -4.83518737548 0.057261950911
34 33.0 -4.89164988211 0.0556538286799
35 34.0 -4.94647694795 0.0539914561312
36 35.0 -4.99961550465 0.0522772186102
37 36.0 -5.05101493277 0.0505136279528
38 37.0 -5.10062718621 0.048703318195
39 38.0 -5.14840691207 0.0468490409338
40 39.0 -5.19431156578 0.0449536603471
41 40.0 -5.23830152101 0.0430201478838
42 41.0 -5.28034017422 0.0410515766363
43 42.0 -5.3203940433 0.0390511154063
44 43.0 -5.35843286021 0.0370220224793
45 44.0 -5.39442965726 0.0349676391193
46 45.0 -5.4283608467 0.0328913828015
47 46.0 -5.46020629342 0.0307967401964
48 47.0 -5.48994938059 0.028687259923
49 48.0 -5.51757706789 0.0265665450883
50 49.0 -5.54307994213 0.0244382456298
51 50.0 -5.56645226024 0.0223060504811
52 51.0 -5.58769198425 0.0201736795783
53 52.0 -5.60680080825 0.0180448757265
54 53.0 -5.62378417713 0.0159233963481
55 54.0 -5.63865129702 0.0138130051308
56 55.0 -5.6514151374 0.0117174635982
57 56.0 -5.66209242462 0.00964052262251
58 57.0 -5.67070362704 0.00758591390103
59 58.0 -5.67727293157 0.00555734141841
60 59.0 -5.6818282117 0.00355847291538
61 60.0 -5.68440098698 0.00159293138608
62 61.0 -5.68502637408 -0.000335713374531
63 62.0 -5.68374302934 -0.00222395315148
64 63.0 -5.68059308309 -0.0040683495974
65 64.0 -5.67562206565 -0.00586554240548
66 65.0 -5.66887882528 -0.00761225734683
67 66.0 -5.66041543813 -0.00930531415106
68 67.0 -5.65028711044 -0.0109416342099
69 68.0 -5.63855207307 -0.0125182480831
70 69.0 -5.6252714687 -0.0140323027883
71 70.0 -5.61050923182 -0.0154810688529
72 71.0 -5.59433196178 -0.0168619471125
73 72.0 -5.57680878923 -0.0181724752358
74 73.0 -5.5580112361 -0.019410333958
75 74.0 -5.53801306959 -0.0205733530082
76 75.0 -5.51689015031 -0.0216595167121
77 76.0 -5.49472027505 -0.0226669692568
78 77.0 -5.47158301441 -0.0235940196022
79 78.0 -5.44755954575 -0.0244391460249
80 79.0 -5.42273248172 -0.0252010002837
81 80.0 -5.3971856949 -0.0258784113929
82 81.0 -5.37100413881 -0.0264703889936
83 82.0 -5.34427366574 -0.0269761263135
84 83.0 -5.31708084192 -0.0273950027051
85 84.0 -5.28951276022 -0.0277265857564
86 85.0 -5.26165685114 -0.0279706329651
87 86.0 -5.23360069216 -0.0281270929735
88 87.0 -5.20543181621 -0.0281961063563
89 88.0 -5.17723751951 -0.0281780059613
90 89.0 -5.14910466934 -0.0280733167983
91 90.0 -5.12111951208 -0.0278827554757
92 91.0 -5.09336748214 -0.0276072291861
93 92.0 -5.06593301201 -0.0272478342399
94 93.0 -5.0388993441 -0.026805854151
95 94.0 -5.01234834466 -0.0262827572773
96 95.0 -4.98636032033 -0.0256801940208
97 96.0 -4.96101383762 -0.0249999935924
98 97.0 -4.93638554598 -0.0242441603499
99 98.0 -4.91255000457 -0.0234148697145
100 99.0 -4.88957951348 -0.0225144636776
101 100.0 -4.86754394953 -0.0215454459053
102 101.0 -4.84651060724 -0.0205104764546
103 102.0 -4.8265440452 -0.01941236611
104 103.0 -4.80770593836 -0.0182540703564
105 104.0 -4.79005493648 -0.0170386830008
106 105.0 -4.77364652914 -0.0157694294583
107 106.0 -4.7585329176 -0.0144496597171
108 107.0 -4.74476289391 -0.0130828410011
109 108.0 -4.73238172744 -0.0116725501446
110 109.0 -4.72143105919 -0.0102224657007
111 110.0 -4.71194880414 -0.00873635979846
112 111.0 -4.70396906182 -0.0072180897712
113 112.0 -4.69752203541 -0.00567158957449
114 113.0 -4.69263395945 -0.00410086101469
115 114.0 -4.68932703648 -0.00250996480925
116 115.0 -4.68761938265 -0.000903011500147
117 116.0 -4.68752498248 0.00071584775762
118 117.0 -4.68905365291 0.00234243051027
119 118.0 -4.69221101668 0.00397253239976
120 119.0 -4.69699848518 0.00560193661579
121 120.0 -4.70341325069 0.00722642338265
122 121.0 -4.71144828821 0.00884177945771
123 122.0 -4.72109236669 0.0104438076188
124 123.0 -4.73233006984 0.0120283361174
125 124.0 -4.74514182625 0.0135912280748
126 125.0 -4.75950394898 0.0151283907985
127 126.0 -4.77538868431 0.0166357849963
128 127.0 -4.79276426974 0.0181094338658
129 128.0 -4.81159500092 0.0195454320375
130 129.0 -4.83184130754 0.0209399543498
131 130.0 -4.8534598378 0.0222892644342
132 131.0 -4.87640355143 0.0235897230915
133 132.0 -4.90062182095 0.0248377964369
134 133.0 -4.92606054096 0.0260300637961
135 134.0 -4.95266224518 0.0271632253326
136 135.0 -4.98036623096 0.028234109388
137 136.0 -5.00910869107 0.0292396795182
138 137.0 -5.03882285221 0.0301770412082
139 138.0 -5.06943912022 0.0310434482505
140 139.0 -5.10088523142 0.0318363087705
141 140.0 -5.13308640979 0.0325531908865
142 141.0 -5.16596552963 0.0331918279898
143 142.0 -5.19944328334 0.0337501236332
144 143.0 -5.23343835383 0.0342261560164
145 144.0 -5.26786759123 0.0346181820585
146 145.0 -5.30264619353 0.0349246410472
147 146.0 -5.33768789051 0.0351441578585
148 147.0 -5.37290513082 0.0352755457383
149 148.0 -5.40820927152 0.0353178086401
150 149.0 -5.4435107698 0.0352701431151
151 150.0 -5.4787193763 0.0351319397498
152 151.0 -5.51374432971 0.0349027841491
153 152.0 -5.54849455206 0.0345824574643
154 153.0 -5.58287884436 0.0341709364636
155 154.0 -5.61680608206 0.0336683931487
156 155.0 -5.65018540988 0.0330751939177
157 156.0 -5.68292643563 0.0323918982779
158 157.0 -5.71493942249 0.0316192571138
159 158.0 -5.74613547931 0.0307582105139
160 159.0 -5.77642674856 0.029809885165
161 160.0 -5.80572659147 0.0287755913197
162 161.0 -5.83394976986 0.0276568193473
163 162.0 -5.86101262442 0.0264552358763
164 163.0 -5.8868332488 0.025172679541
165 164.0 -5.91133165941 0.0238111563427
166 165.0 -5.93442996024 0.0223728346376
167 166.0 -5.95605250261 0.0208600397671
168 167.0 -5.97612603931 0.0192752483425
169 168.0 -5.99457987285 0.0176210822011
170 169.0 -6.01134599757 0.015900302049
171 170.0 -6.02635923519 0.014115800807
172 171.0 -6.03955736358 0.0122705966784
173 172.0 -6.05088123845 0.0103678259555
174 173.0 -6.0602749078 0.00841073558436
175 174.0 -6.06768571866 0.00640267550713
176 175.0 -6.0730644163 0.00434709080102
177 176.0 -6.07636523524 0.00224751363529
178 177.0 -6.07754598232 0.000107555066143
179 178.0 -6.07656811141 -0.00206910330914
180 179.0 -6.07339678973 -0.00427871781763
181 180.0 -6.06800095563 -0.00651749127408
182 181.0 -6.06035336781 -0.00878158162059
183 182.0 -6.05043064586 -0.0110671106207
184 183.0 -6.03821330204 -0.0133701725859
185 184.0 -6.02368576439 -0.0156868431131
186 185.0 -6.00683639108 -0.0180131878107
187 186.0 -5.98765747603 -0.0203452709919
188 187.0 -5.96614524589 -0.0226791643135
189 188.0 -5.94229984843 -0.025010955339
190 189.0 -5.91612533236 -0.0273367560054
191 190.0 -5.88762961878 -0.0296527109716
192 191.0 -5.85682446433 -0.0319550058299
193 192.0 -5.82372541626 -0.0342398751598
194 193.0 -5.78835175943 -0.0365036104045
195 194.0 -5.75072645562 -0.0387425675516
196 195.0 -5.71087607524 -0.0409531746008
197 196.0 -5.66883072166 -0.0431319387984
198 197.0 -5.62462394846 -0.0452754536249
199 198.0 -5.57829266983 -0.0473804055171
200 199.0 -5.5298770643 -0.0494435803104
201 200.0 -5.47942047235 -0.0514618693867
202 201.0 -5.42696928781 -0.0534322755136
203 202.0 -5.37257284377 -0.055351918363
204 203.0 -5.316283293 -0.0572180396955
205 204.0 -5.25815548345 -0.059028008202
206 205.0 -5.19824682901 -0.0607793239895
207 206.0 -5.13661717604 -0.0624696227052
208 207.0 -5.0733286659 -0.0640966792879
209 208.0 -5.00844559393 -0.0656584113417
210 209.0 -4.94203426529 -0.0671528821253
211 210.0 -4.87416284794 -0.0685783031513
212 211.0 -4.80490122327 -0.0699330363936
213 212.0 -4.7343208347 -0.0712155960973
214 213.0 -4.66249453466 -0.0724246501921
215 214.0 -4.58949643037 -0.0735590213066
216 215.0 -4.51540172879 -0.0746176873849
217 216.0 -4.44028658118 -0.0755997819067
218 217.0 -4.3642279276 -0.0765045937139
219 218.0 -4.28730334182 -0.0773315664459
220 219.0 -4.20959087694 -0.0780802975905
221 220.0 -4.13116891218 -0.0787505371538
222 221.0 -4.0521160012 -0.0793421859574
223 222.0 -3.97251072229 -0.0798552935693
224 223.0 -3.89243153076 -0.0802900558785
225 224.0 -3.81195661404 -0.0806468123209
226 225.0 -3.73116374964 -0.0809260427693
227 226.0 -3.65013016636 -0.0811283640964
228 227.0 -3.56893240921 -0.0812545264246
229 228.0 -3.48764620813 -0.0813054090744
230 229.0 -3.4063463509 -0.0812820162266
231 230.0 -3.32510656064 -0.0811854723104
232 231.0 -3.24399937793 -0.081017017134
233 232.0 -3.16309604794 -0.0807780007742
234 233.0 -3.08246641287 -0.0804698782381
235 234.0 -3.00217880976 -0.0800942039176
236 235.0 -2.92229997393 -0.079652625851
237 236.0 -2.84289494829 -0.0791468798106
238 237.0 -2.76402699866 -0.0785787832348
239 238.0 -2.68575753514 -0.0779502290223
240 239.0 -2.60814603984 -0.077263179207
241 240.0 -2.53125000097 -0.0765196585342
242 241.0 -2.4551248533 -0.0757217479546
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360 359.0 -2.48521512832 0.072569481568

988
tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.6.dat
View File

@ -1,988 +0,0 @@
# 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 3.66 115.071648949 1922.94202847
114 3.665 105.862676198 1763.11994431
115 3.67 97.4169155884 1617.42319704
116 3.675 89.6671295106 1484.51973131
117 3.68 82.5523999227 1363.21125435
118 3.685 76.0174958886 1252.41898087
119 3.69 70.0123082899 1151.17098442
120 3.695 64.4913441675 1058.59096449
121 3.7 59.4132740402 973.88826227
122 3.705 54.7405263329 896.348978842
123 3.71 50.438923727 825.328067481
124 3.715 46.4773568526 760.242287449
125 3.72 42.8274912666 700.563920374
126 3.725 39.4635041252 645.815162231
127 3.73 36.3618473701 595.563114331
128 3.735 33.5010346035 549.415305905
129 3.74 30.8614491473 507.015688796
130 3.745 28.425171059 468.041051794
131 3.75 26.1758211241 432.197808262
132 3.755 24.0984200646 399.21911609
133 3.76 22.179261392 368.86229374
134 3.765 20.4057965086 340.906500282
135 3.77 18.7665308078 315.150650994
136 3.775 17.2509296613 291.411543325
137 3.78 15.8493332971 269.522170811
138 3.785 14.5528796804 249.330205101
139 3.79 13.3534346012 230.696628411
140 3.795 12.2435282565 213.494500686
141 3.8 11.2162976896 197.607847495
142 3.805 10.2654345142 182.930656184
143 3.81 9.38513741093 169.365969178
144 3.815 8.57006893443 156.825064535
145 3.82 7.81531621929 145.226714879
146 3.825 7.1163552113 134.496516825
147 3.83 6.46901809043 124.566283826
148 3.835 5.86946358438 115.373496111
149 3.84 5.3141499016 106.860802062
150 3.845 4.79981003946 98.9755659598
151 3.85 4.32342924744 91.6694575494
152 3.855 3.88222444642 84.8980793495
153 3.86 3.47362542484 78.6206280516
154 3.865 3.09525764949 72.7995867184
155 3.87 2.74492654463 67.4004448293
156 3.875 2.42060310675 62.3914435192
157 3.88 2.12041073521 57.7433436194
158 3.885 1.84261317026 53.4292143513
159 3.89 1.58560343996 49.424240734
160 3.895 1.34789372698 45.7055479593
161 3.9 1.12810607442 42.2520411601
162 3.905 0.92496385733 39.0442591487
163 3.91 0.737283953249 36.0642408427
164 3.915 0.563969551396 33.2954032193
165 3.92 0.404003545437 30.7224297483
166 3.925 0.2564424599 28.3311683573
167 3.93 0.120410864734 26.1085380703
168 3.935 -0.00490376337106 24.0424435434
169 3.94 -0.120255770611 22.1216967943
170 3.945 -0.226345680979 20.3359454863
171 3.95 -0.323824207772 18.6756071913
172 3.955 -0.413295950251 17.1318091041
173 3.96 -0.495322801504 15.6963327338
174 3.965 -0.570427091298 14.3615631388
175 3.97 -0.639094485635 13.1204423129
176 3.975 -0.701776662868 11.9664263642
177 3.98 -0.75889378451 10.8934461632
178 3.985 -0.810836777335 9.89587116294
179 3.99 -0.857969441941 8.96847612349
180 3.995 -0.900630401683 8.10641049364
181 4.0 -0.939134904689 7.30517022808
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183 4.01 -1.00482853285 5.86872847094
184 4.015 -1.03254566588 5.22602790624
185 4.02 -1.05716510696 4.62911221801
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978 7.985 -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

989
tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.dat
View File

@ -1,989 +0,0 @@
# 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 3117.93407879
109 3.64 179.663555764 2856.60118023
110 3.645 165.984079802 2618.93405823
111 3.65 153.438619766 2402.63212994
112 3.655 141.925598023 2205.6335579
113 3.66 131.353204775 2026.08892777
114 3.665 121.638395266 1862.33799643
115 3.67 112.705996374 1712.88913275
116 3.675 104.487909965 1576.40112248
117 3.68 96.9224019089 1451.66705065
118 3.685 89.9534670245 1337.6000114
119 3.69 83.5302613658 1233.22042683
120 3.695 77.6065942935 1137.6447839
121 3.7 72.1404736708 1050.07562216
122 3.705 67.0936983024 969.792625804
123 3.71 62.431492423 896.144691745
124 3.715 58.1221776441 828.54286083
125 3.72 54.1368782948 766.454013201
126 3.725 50.4492565603 709.395240693
127 3.73 47.0352742263 656.928819585
128 3.735 43.8729782026 608.65771617
129 3.74 40.9423073113 564.221565572
130 3.745 38.2249181088 523.293071279
131 3.75 35.7040277571 485.57477893
132 3.755 33.3642721761 450.796183363
133 3.76 31.1915779041 418.711132572
134 3.765 29.1730462649 389.095496464
135 3.77 27.296848588 361.745071901
136 3.775 25.5521313672 336.473698771
137 3.78 23.9289303577 313.111564661
138 3.785 22.4180927206 291.503678217
139 3.79 21.0112064166 271.508493474
140 3.795 19.7005361332 252.996669413
141 3.8 18.4789651059 235.849950713
142 3.805 17.3399422592 219.960157211
143 3.81 16.2774341511 205.228270919
144 3.815 15.2858812611 191.563610676
145 3.82 14.3601582029 178.88308554
146 3.825 13.4955374911 167.110519006
147 3.83 12.6876565243 156.176036954
148 3.835 11.9324874825 146.015512988
149 3.84 11.2263098661 136.570065484
150 3.845 10.5656854316 127.785601256
151 3.85 9.94743530166 119.612401285
152 3.855 9.36861904981 112.004744426
153 3.86 8.82651557999 104.920565393
154 3.865 8.31860563683 98.3211437563
155 3.87 7.84255579999 92.1708209642
156 3.875 7.39620382887 86.4367427306
157 3.88 6.97754523696 81.0886243871
158 3.885 6.58472098661 76.0985370389
159 3.89 6.21600620515 71.4407125773
160 3.895 5.86979983242 67.0913657925
161 3.9 5.54461511838 63.0285320059
162 3.905 5.23907089671 59.2319187891
163 3.91 4.95188356739 55.6827704829
164 3.915 4.68185972707 52.3637443466
165 3.92 4.42788939186 49.2587972858
166 3.925 4.18893976204 46.353082203
167 3.93 3.96404948281 43.6328531095
168 3.935 3.75232335915 41.0853782151
169 3.94 3.55292748687 38.6988602882
170 3.945 3.36508476491 36.4623636443
171 3.95 3.18807075749 34.3657471793
172 3.955 3.021209877 32.3996029206
173 3.96 2.86387186138 30.5551996145
174 3.965 2.71546852189 28.8244309147
175 3.97 2.57545073925 27.1997677761
176 3.975 2.44330568809 25.6742146917
177 3.98 2.31855427126 24.2412694474
178 3.985 2.20074874724 22.8948860937
179 3.99 2.08947053515 21.6294408646
180 3.995 1.98432818342 20.4397007945
181 4.0 1.88495548901 19.3207948084
182 4.005 1.79100975549 18.2681870794
183 4.01 1.70217017901 17.2776524655
184 4.015 1.61813635232 16.3452538542
185 4.02 1.53862687753 15.467321259
186 4.025 1.4633780794 14.6404325234
187 4.03 1.3921428113 13.8613955037
188 4.035 1.32468934683 13.1272316094
189 4.04 1.26080035064 12.435160592
190 4.045 1.20027192224 11.7825864834
191 4.05 1.14291270762 11.1670845906
192 4.055 1.08854307328 10.5863894642
193 4.06 1.03699433825 10.0383837622
194 4.065 0.988108059646 9.5210879405
195 4.07 0.941735367837 9.03265070365
196 4.075 0.897736347632 8.57134015767
197 4.08 0.855979462015 8.13553560989
198 4.085 0.816341015387 7.72371996598
199 4.09 0.778704653425 7.33447267828
200 4.095 0.74296089691 6.96646320305
201 4.1 0.709006707075 6.61844492796
202 4.105 0.676745080218 6.28924953404
203 4.11 0.646084669489 5.97778175928
204 4.115 0.616939431912 5.68301453361
205 4.12 0.589228298872 5.40398445752
206 4.125 0.562874868393 5.13978759855
207 4.13 0.537807117698 4.88957558211
208 4.135 0.513957134618 4.65255195486
209 4.14 0.491260866548 4.42796880052
210 4.145 0.469657885731 4.21512358966
211 4.15 0.449091169745 4.01335624628
212 4.155 0.429506896145 3.82204641559
213 4.16 0.410854250299 3.64061091811
214 4.165 0.393085245513 3.46850137704
215 4.17 0.376154554607 3.30520200609
216 4.175 0.360019352187 3.15022754657
217 4.18 0.34463916687 3.00312134286
218 4.185 0.329975742808 2.86345354671
219 4.19 0.315992909894 2.730819441
220 4.195 0.30265646206 2.60483787474
221 4.2 0.289934043143 2.48514980144
222 4.205 0.277795039817 2.37141691363
223 4.21 0.26621048112 2.26332036686
224 4.215 0.255152944156 2.160559587
225 4.22 0.244596465565 2.06285115501
226 4.225 0.234516458378 1.96992776403
227 4.23 0.22488963393 1.88153724361
228 4.235 0.215693928479 1.79744164671
229 4.24 0.206908434252 1.71741639508
230 4.245 0.198513334625 1.64124947915
231 4.25 0.190489843169 1.56874070868
232 4.255 0.182820146331 1.49970101084
233 4.26 0.175487349508 1.43395177247
234 4.265 0.168475426305 1.3713242237
235 4.27 0.16176917078 1.31165886002
236 4.275 0.155354152487 1.2548049004
237 4.28 0.149216674142 1.20061977901
238 4.285 0.143343731751 1.1489686684
239 4.29 0.137722977049 1.09972403198
240 4.295 0.13234268211 1.05276520399
241 4.3 0.127191705983 1.00797799517
242 4.305 0.122259463251 0.965254322417
243 4.31 0.117535894375 0.924491860866
244 4.315 0.113011437731 0.885593717092
245 4.32 0.108677003225 0.848468121932
246 4.325 0.104523947407 0.813028141752
247 4.33 0.100544049971 0.779191406981
248 4.335 0.0967294915884 0.746879856814
249 4.34 0.0930728329625 0.716019499063
250 4.345 0.0895669950612 0.686540184216
251 4.35 0.0862052404384 0.658375392808
252 4.355 0.08298115559 0.63146203527
253 4.36 0.0798886342796 0.605740263498
254 4.365 0.0769218617798 0.5811532934
255 4.37 0.0740752999737 0.557647237752
256 4.375 0.0713436732684 0.535170948731
257 4.38 0.0687219552728 0.513675869532
258 4.385 0.0662053561949 0.493115894506
259 4.39 0.0637893109199 0.473447237321
260 4.395 0.0614694677263 0.45462830664
261 4.4 0.0592416776079 0.436619588871
262 4.405 0.0571019841636 0.419383537567
263 4.41 0.0550466140255 0.402884469071
264 4.415 0.0530719677933 0.387088464035
265 4.42 0.0511746114473 0.371963274467
266 4.425 0.0493512682135 0.357478235973
267 4.43 0.0475988108542 0.343604184887
268 4.435 0.0459142543625 0.33031338001
269 4.44 0.0442947490359 0.317579428671
270 4.445 0.0427375739105 0.305377216875
271 4.45 0.041240130534 0.293682843283
272 4.455 0.0397999370598 0.282473556818
273 4.46 0.0384146226445 0.271727697674
274 4.465 0.0370819221326 0.261424641529
275 4.47 0.035799671012 0.251544746799
276 4.475 0.034565800626 0.242069304731
277 4.48 0.0333783336288 0.232980492193
278 4.485 0.0322353796696 0.224261326994
279 4.49 0.0311351312947 0.215895625604
280 4.495 0.0300758600554 0.207867963122
281 4.5 0.0290559128103 0.200163635378
282 4.505 0.0280737082121 0.192768623045
283 4.51 0.0271277333693 0.185669557645
284 4.515 0.0262165406731 0.178853689349
285 4.52 0.0253387447812 0.172308856461
286 4.525 0.0244930197498 0.166023456513
287 4.53 0.023678096307 0.159986418851
288 4.535 0.0228927592589 0.154187178661
289 4.54 0.0221358450227 0.148615652333
290 4.545 0.0214062392796 0.143262214105
291 4.55 0.0207028747413 0.138117673905
292 4.555 0.0200247290247 0.133173256332
293 4.56 0.0193708226289 0.128420580717
294 4.565 0.018740217009 0.123851642198
295 4.57 0.0181320127424 0.119458793758
296 4.575 0.017545347783 0.115234729179
297 4.58 0.0169793957974 0.111172466848
298 4.585 0.0164333645811 0.107265334394
299 4.59 0.0159064945488 0.103506954082
300 4.595 0.0153980572965 0.0998912289493
301 4.6 0.0149073542304 0.0964123296321
302 4.605 0.0144337152611 0.0930646818445
303 4.61 0.0139764975575 0.0898429544837
304 4.615 0.0135350843599 0.086742048322
305 4.62 0.0131088838475 0.0837570852568
306 4.625 0.0126973280587 0.0808833980908
307 4.63 0.0122998718608 0.0781165208124
308 4.635 0.0119159919677 0.0754521793521
309 4.64 0.0115451860021 0.07288628279
310 4.645 0.0111869716011 0.0704149149899
311 4.65 0.010840885562 0.0680343266405
312 4.655 0.0105064830275 0.0657409276799
313 4.66 0.0101833367076 0.063531280086
314 4.665 0.0098710361368 0.0614020910133
315 4.67 0.00956918696433 0.0593502062585
316 4.675 0.00927741027701 0.0573726040383
317 4.68 0.00899534195191 0.0554663890638
318 4.685 0.00872263203811 0.0536287868959
319 4.69 0.00845894416602 0.0518571385691
320 4.695 0.0082039549829 0.0501488954678
321 4.7 0.00795735361347 0.0485016144454
322 4.705 0.00771884114422 0.0469129531714
323 4.71 0.00748813013054 0.045380665697
324 4.715 0.00726494412547 0.0439025982277
325 4.72 0.00704901722906 0.0424766850927
326 4.725 0.00684009365745 0.0411009449015
327 4.73 0.00663792733071 0.0397734768782
328 4.735 0.00644228147858 0.0384924573653
329 4.74 0.00625292826325 0.0372561364888
330 4.745 0.00606964841851 0.0360628349754
331 4.75 0.00589223090433 0.0349109411165
332 4.755 0.00572047257643 0.0337989078704
333 4.76 0.0055541778698 0.0327252500962
334 4.765 0.00539315849596 0.0316885419138
335 4.77 0.00523723315293 0.0306874141829
336 4.775 0.00508622724762 0.0297205520964
337 4.78 0.00493997262995 0.0287866928817
338 4.785 0.00479830733822 0.0278846236056
339 4.79 0.00466107535518 0.0270131790775
340 4.795 0.00452812637438 0.0261712398457
341 4.8 0.00439931557628 0.0253577302837
342 4.805 0.00427450341372 0.0245716167613
343 4.81 0.00415355540638 0.0238119058963
344 4.815 0.00403634194372 0.0230776428841
345 4.82 0.00392273809612 0.0223679099007
346 4.825 0.00381262343384 0.0216818245753
347 4.83 0.00370588185338 0.021018538531
348 4.835 0.00360240141109 0.0203772359884
349 4.84 0.00350207416352 0.0197571324301
350 4.845 0.0034047960143 0.019157473324
351 4.85 0.00331046656734 0.0185775329012
352 4.855 0.00321898898591 0.0180166129873
353 4.86 0.00313026985753 0.0174740418837
354 4.865 0.00304421906424 0.0169491732974
355 4.87 0.00296074965818 0.0164413853165
356 4.875 0.00287977774216 0.0159500794299
357 4.88 0.002801222355 0.0154746795881
358 4.885 0.0027250053615 0.0150146313053
359 4.89 0.00265105134676 0.0145694007979
360 4.895 0.0025792875148 0.0141384741613
361 4.9 0.00250964359108 0.0137213565802
362 4.905 0.00244205172902 0.0133175715727
363 4.91 0.00237644642012 0.0129266602662
364 4.915 0.00231276440768 0.0125481807036
365 4.92 0.00225094460389 0.0121817071786
366 4.925 0.00219092801016 0.0118268295982
367 4.93 0.00213265764061 0.011483152873
368 4.935 0.00207607844856 0.011150296331
369 4.94 0.00202113725576 0.0108278931578
370 4.945 0.00196778268457 0.0105155898576
371 4.95 0.00191596509257 0.0102130457388
372 4.955 0.00186563650984 0.00991993241864
373 4.96 0.0018167505786 0.00963593334953
374 4.965 0.00176926249515 0.0093607433642
375 4.97 0.0017231289541 0.00909406823946
376 4.975 0.00167830809471 0.00883562427782
377 4.98 0.00163475944922 0.00858513790595
378 4.985 0.00159244389324 0.00834234528958
379 4.99 0.001551323598 0.00810699196376
380 4.995 0.00151136198435 0.00787883247819
381 5.0 0.00147252367858 0.00765763005674
382 5.005 0.00143477446984 0.00744315627058
383 5.01 0.00139808126924 0.00723519072448
384 5.015 0.00136241207038 0.00703352075553
385 5.02 0.00132773591148 0.00683794114397
386 5.025 0.00129402283882 0.00664825383541
387 5.03 0.00126124387159 0.00646426767408
388 5.035 0.00122937096804 0.00628579814667
389 5.04 0.00119837699293 0.00611266713619
390 5.045 0.00116823568608 0.00594470268561
391 5.05 0.00113892163217 0.00578173877069
392 5.055 0.00111041023163 0.00562361508175
393 5.06 0.00108267767261 0.00547017681395
394 5.065 0.00105570090391 0.00532127446577
395 5.07 0.00102945760901 0.00517676364527
396 5.075 0.00100392618096 0.00503650488393
397 5.08 0.000979085698203 0.00490036345763
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739 6.79 1.71931988509e-06 5.05865498999e-06
740 6.795 1.69421800875e-06 4.98230547687e-06
741 6.8 1.66949474959e-06 4.90720441581e-06
742 6.805 1.6451439205e-06 4.83332982211e-06
743 6.81 1.62115944323e-06 4.76066012583e-06
744 6.815 1.59753534637e-06 4.68917416347e-06
745 6.82 1.57426576334e-06 4.61885116973e-06
746 6.825 1.55134493038e-06 4.54967076962e-06
747 6.83 1.52876718466e-06 4.48161297055e-06
748 6.835 1.50652696239e-06 4.41465815471e-06
749 6.84 1.48461879691e-06 4.3487870716e-06
750 6.845 1.46303731695e-06 4.28398083065e-06
751 6.85 1.44177724478e-06 4.22022089406e-06
752 6.855 1.42083339451e-06 4.15748906981e-06
753 6.86 1.40020067034e-06 4.09576750471e-06
754 6.865 1.37987406492e-06 4.03503867774e-06
755 6.87 1.35984865768e-06 3.97528539342e-06
756 6.875 1.34011961322e-06 3.91649077535e-06
757 6.88 1.32068217977e-06 3.85863825993e-06
758 6.885 1.30153168756e-06 3.80171159016e-06
759 6.89 1.2826635474e-06 3.74569480958e-06
760 6.895 1.26407324911e-06 3.69057225636e-06
761 6.9 1.2457563601e-06 3.63632855747e-06
762 6.905 1.22770852394e-06 3.58294862303e-06
763 6.91 1.20992545896e-06 3.53041764074e-06
764 6.915 1.19240295686e-06 3.47872107044e-06
765 6.92 1.17513688137e-06 3.42784463875e-06
766 6.925 1.15812316694e-06 3.37777433388e-06
767 6.93 1.14135781743e-06 3.32849640049e-06
768 6.935 1.12483690484e-06 3.27999733473e-06
769 6.94 1.10855656808e-06 3.23226387928e-06
770 6.945 1.09251301173e-06 3.18528301858e-06
771 6.95 1.07670250488e-06 3.13904197413e-06
772 6.955 1.06112137989e-06 3.09352819987e-06
773 6.96 1.0457660313e-06 3.0487293777e-06
774 6.965 1.03063291469e-06 3.00463341302e-06
775 6.97 1.01571854555e-06 2.96122843043e-06
776 6.975 1.0010194982e-06 2.9185027695e-06
777 6.98 9.86532404745e-07 2.87644498061e-06
778 6.985 9.72253954022e-07 2.83504382088e-06
779 6.99 9.58180890566e-07 2.79428825018e-06
780 6.995 9.44310013618e-07 2.75416742728e-06
781 7.0 9.30638176135e-07 2.71467070595e-06
782 7.005 9.17162283824e-07 2.6757876313e-06
783 7.01 9.03879294199e-07 2.63750793605e-06
784 7.015 8.90786215647e-07 2.59982153697e-06
785 7.02 8.77880106517e-07 2.56271853136e-06
786 7.025 8.6515807423e-07 2.5261891936e-06
787 7.03 8.52617274397e-07 2.49022397175e-06
788 7.035 8.40254909964e-07 2.4548134843e-06
789 7.04 8.28068230364e-07 2.41994851684e-06
790 7.045 8.16054530689e-07 2.38562001899e-06
791 7.05 8.04211150882e-07 2.35181910119e-06
792 7.055 7.92535474938e-07 2.3185370317e-06
793 7.06 7.81024930121e-07 2.28576523364e-06
794 7.065 7.696769862e-07 2.25349528197e-06
795 7.07 7.58489154692e-07 2.22171890072e-06
796 7.075 7.47458988133e-07 2.19042796013e-06
797 7.08 7.36584079342e-07 2.15961447389e-06
798 7.085 7.2586206072e-07 2.12927059646e-06
799 7.09 7.15290603549e-07 2.09938862041e-06
800 7.095 7.04867417307e-07 2.06996097384e-06
801 7.1 6.94590249e-07 2.04098021782e-06
802 7.105 6.84456882499e-07 2.01243904392e-06
803 7.11 6.74465137898e-07 1.98433027176e-06
804 7.115 6.64612870877e-07 1.9566468466e-06
805 7.12 6.5489797208e-07 1.92938183703e-06
806 7.125 6.45318366505e-07 1.90252843264e-06
807 7.13 6.35872012904e-07 1.87607994179e-06
808 7.135 6.26556903196e-07 1.85002978938e-06
809 7.14 6.17371061887e-07 1.8243715147e-06
810 7.145 6.08312545506e-07 1.7990987693e-06
811 7.15 5.99379442048e-07 1.77420531491e-06
812 7.155 5.90569870428e-07 1.74968502142e-06
813 7.16 5.81881979945e-07 1.72553186483e-06
814 7.165 5.73313949757e-07 1.70173992537e-06
815 7.17 5.64863988364e-07 1.67830338549e-06
816 7.175 5.56530333103e-07 1.65521652804e-06
817 7.18 5.4831124965e-07 1.63247373439e-06
818 7.185 5.40205031528e-07 1.61006948263e-06
819 7.19 5.32209999637e-07 1.58799834581e-06
820 7.195 5.24324501773e-07 1.56625499017e-06
821 7.2 5.16546912175e-07 1.54483417343e-06
822 7.205 5.08875631066e-07 1.52373074317e-06
823 7.21 5.01309084211e-07 1.50293963511e-06
824 7.215 4.93845722479e-07 1.48245587157e-06
825 7.22 4.86484021414e-07 1.46227455985e-06
826 7.225 4.79222480814e-07 1.44239089069e-06
827 7.23 4.72059624319e-07 1.42280013677e-06
828 7.235 4.64993999004e-07 1.4034976512e-06
829 7.24 4.58024174978e-07 1.38447886607e-06
830 7.245 4.51148744997e-07 1.36573929102e-06
831 7.25 4.44366324079e-07 1.34727451183e-06
832 7.255 4.37675549122e-07 1.32908018904e-06
833 7.26 4.31075078542e-07 1.31115205663e-06
834 7.265 4.24563591899e-07 1.29348592063e-06
835 7.27 4.1813978955e-07 1.2760776579e-06
836 7.275 4.11802392291e-07 1.25892321479e-06
837 7.28 4.05550141016e-07 1.24201860594e-06
838 7.285 3.99381796376e-07 1.22535991301e-06
839 7.29 3.9329613845e-07 1.20894328352e-06
840 7.295 3.87291966418e-07 1.19276492962e-06
841 7.3 3.81368098239e-07 1.17682112698e-06
842 7.305 3.75523370336e-07 1.16110821364e-06
843 7.31 3.69756637291e-07 1.14562258888e-06
844 7.315 3.64066771537e-07 1.13036071214e-06
845 7.32 3.58452663062e-07 1.11531910195e-06
846 7.325 3.52913219116e-07 1.10049433488e-06
847 7.33 3.47447363922e-07 1.0858830445e-06
848 7.335 3.42054038397e-07 1.07148192036e-06
849 7.34 3.3673219987e-07 1.05728770703e-06
850 7.345 3.31480821814e-07 1.04329720308e-06
851 7.35 3.26298893574e-07 1.02950726017e-06
852 7.355 3.21185420107e-07 1.01591478207e-06
853 7.36 3.16139421723e-07 1.00251672378e-06
854 7.365 3.1115993383e-07 9.89310090577e-07
855 7.37 3.06246006687e-07 9.76291937184e-07
856 7.375 3.01396705156e-07 9.63459366859e-07
857 7.38 2.96611108464e-07 9.50809530558e-07
858 7.385 2.91888309966e-07 9.38339626099e-07
859 7.39 2.87227416913e-07 9.26046897331e-07
860 7.395 2.82627550221e-07 9.13928633336e-07
861 7.4 2.78087844251e-07 9.01982167635e-07
862 7.405 2.73607446588e-07 8.90204877406e-07
863 7.41 2.6918551782e-07 8.78594182731e-07
864 7.415 2.64821231333e-07 8.67147545837e-07
865 7.42 2.60513773095e-07 8.55862470371e-07
866 7.425 2.56262341455e-07 8.44736500673e-07
867 7.43 2.5206614694e-07 8.33767221072e-07
868 7.435 2.47924412057e-07 8.22952255188e-07
869 7.44 2.43836371097e-07 8.12289265255e-07
870 7.445 2.39801269946e-07 8.01775951447e-07
871 7.45 2.35818365896e-07 7.91410051224e-07
872 7.455 2.31886927457e-07 7.81189338689e-07
873 7.46 2.28006234181e-07 7.7111162395e-07
874 7.465 2.2417557648e-07 7.61174752504e-07
875 7.47 2.20394255452e-07 7.51376604623e-07
876 7.475 2.16661582706e-07 7.41715094759e-07
877 7.48 2.12976880196e-07 7.32188170953e-07
878 7.485 2.09339480053e-07 7.22793814262e-07
879 7.49 2.05748724421e-07 7.13530038185e-07
880 7.495 2.02203965296e-07 7.04394888118e-07
881 7.5 1.9870456437e-07 6.95386440797e-07
882 7.505 1.95249892873e-07 6.86502803769e-07
883 7.51 1.91839331421e-07 6.77742114863e-07
884 7.515 1.88472269866e-07 6.69102541673e-07
885 7.52 1.85148107151e-07 6.60582281052e-07
886 7.525 1.8186625116e-07 6.52179558612e-07
887 7.53 1.7862611858e-07 6.43892628236e-07
888 7.535 1.75427134757e-07 6.35719771598e-07
889 7.54 1.72268733561e-07 6.27659297689e-07
890 7.545 1.6915035725e-07 6.19709542357e-07
891 7.55 1.66071456337e-07 6.11868867849e-07
892 7.555 1.63031489458e-07 6.04135662368e-07
893 7.56 1.60029923244e-07 5.96508339628e-07
894 7.565 1.57066232194e-07 5.88985338432e-07
895 7.57 1.54139898552e-07 5.81565122242e-07
896 7.575 1.51250412185e-07 5.74246178766e-07
897 7.58 1.48397270459e-07 5.6702701955e-07
898 7.585 1.45579978125e-07 5.59906179576e-07
899 7.59 1.42798047202e-07 5.52882216872e-07
900 7.595 1.40050996861e-07 5.4595371212e-07
901 7.6 1.37338353314e-07 5.39119268281e-07
902 7.605 1.34659649703e-07 5.32377510221e-07
903 7.61 1.32014425993e-07 5.25727084341e-07
904 7.615 1.29402228861e-07 5.19166658223e-07
905 7.62 1.26822611598e-07 5.12694920274e-07
906 7.625 1.24275133998e-07 5.06310579376e-07
907 7.63 1.21759362262e-07 5.0001236455e-07
908 7.635 1.19274868896e-07 4.93799024619e-07
909 7.64 1.16821232612e-07 4.87669327877e-07
910 7.645 1.14398038233e-07 4.8162206177e-07
911 7.65 1.120048766e-07 4.75656032572e-07
912 7.655 1.09641344473e-07 4.69770065082e-07
913 7.66 1.07307044442e-07 4.63963002309e-07
914 7.665 1.05001584841e-07 4.58233705177e-07
915 7.67 1.02724579651e-07 4.52581052224e-07
916 7.675 1.0047564842e-07 4.47003939317e-07
917 7.68 9.82544161708e-08 4.41501279361e-07
918 7.685 9.60605133226e-08 4.36072002025e-07
919 7.69 9.38935756035e-08 4.30715053459e-07
920 7.695 9.17532439703e-08 4.25429396028e-07
921 7.7 8.96391645283e-08 4.20214008047e-07
922 7.705 8.75509884516e-08 4.15067883513e-07
923 7.71 8.54883719059e-08 4.09990031857e-07
924 7.715 8.34509759714e-08 4.04979477684e-07
925 7.72 8.14384665682e-08 4.00035260529e-07
926 7.725 7.94505143815e-08 3.95156434615e-07
927 7.73 7.74867947896e-08 3.90342068606e-07
928 7.735 7.55469877916e-08 3.85591245382e-07
929 7.74 7.36307779372e-08 3.80903061797e-07
930 7.745 7.17378542573e-08 3.76276628463e-07
931 7.75 6.9867910196e-08 3.71711069515e-07
932 7.755 6.80206435432e-08 3.67205522401e-07
933 7.76 6.61957563687e-08 3.62759137662e-07
934 7.765 6.43929549576e-08 3.5837107872e-07
935 7.77 6.26119497457e-08 3.54040521671e-07
936 7.775 6.08524552575e-08 3.49766655078e-07
937 7.78 5.91141900435e-08 3.45548679773e-07
938 7.785 5.73968766201e-08 3.41385808656e-07
939 7.79 5.57002414093e-08 3.37277266505e-07
940 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

24
tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.min
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@ -1,24 +0,0 @@
# -- 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

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tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.nvt
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# -- 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

29
tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README.TXT
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# 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

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# 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

24
tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_setup.sh
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# 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 ../

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------- 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.)

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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

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# 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

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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

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#!/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))

20
tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/system.lt
View File

@ -1,20 +0,0 @@
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
}

735
tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/table_dihedral_frustrated.dat
View File

@ -1,735 +0,0 @@
# 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 0.030335275675
49 48.0 -5.90793817411 0.0280229658805
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52 51.0 -5.98153767519 0.0210355766777
53 52.0 -6.00140652074 0.0187025495211
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59 58.0 -6.07203378786 0.00493803637051
60 59.0 -6.07586001075 0.00271939959245
61 60.0 -6.07748320034 0.000532601003776
62 61.0 -6.07693707962 -0.00161859899905
63 62.0 -6.07425910291 -0.00373049957158
64 63.0 -6.06949039207 -0.00579946791801
65 64.0 -6.06267566421 -0.00782194767468
66 65.0 -6.05386315117 -0.00979446715893
67 66.0 -6.04310451074 -0.0117136474624
68 67.0 -6.03045472992 -0.0135762103679
69 68.0 -6.01597202036 -0.0153789860691
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71 70.0 -5.98175610439 -0.0187930834719
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97 96.0 -5.17580883839 -0.0333654175598
98 97.0 -5.14274430152 -0.0327503332496
99 98.0 -5.11033446814 -0.0320563659092
100 99.0 -5.07865712698 -0.0312857323082
101 100.0 -5.04778776623 -0.0304408159764
102 101.0 -5.01779940929 -0.0295241620384
103 102.0 -4.98876245596 -0.0285384716647
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131 130.0 -4.74095420961 0.0126700697544
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332 331.0 -0.906336334692 0.0441356272615
333 332.0 -0.951196567028 0.045584604448
334 333.0 -0.997504838648 0.0470314640498
335 334.0 -1.04525829294 0.048474714408
336 335.0 -1.09445254125 0.0499127835288
337 336.0 -1.1450815839 0.0513440218749
338 337.0 -1.1971377342 0.0527667054614
339 338.0 -1.25061154564 0.0541790392498
340 339.0 -1.30549174267 0.0555791608316
341 340.0 -1.36176515529 0.0569651443923
342 341.0 -1.41941665773 0.0583350049463
343 342.0 -1.47842911151 0.0596867028317
344 343.0 -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 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
11 10.0 -3.30856942003 0.0758590850738
12 11.0 -3.38438599377 0.0757623292865
13 12.0 -3.46007047791 0.0755947754951
14 13.0 -3.53555170381 0.0753557030426
15 14.0 -3.61075784476 0.0750445172025
16 15.0 -3.68561654392 0.0746607529305
17 16.0 -3.76005504566 0.0742040783151
18 17.0 -3.83400033034 0.0736742977129
19 18.0 -3.907379252 0.0730713545594
20 19.0 -3.98011867868 0.0723953338429
21 20.0 -4.0521456351 0.0716464642332
22 21.0 -4.12338744726 0.0708251198546
23 22.0 -4.19377188857 0.0699318216967
24 23.0 -4.26322732737 0.0689672386556
25 24.0 -4.33168287509 0.0679321881993
26 25.0 -4.39906853508 0.0668276366524
27 26.0 -4.46531535141 0.0656546990963
28 27.0 -4.53035555742 0.0644146388823
29 28.0 -4.59412272358 0.0631088667546
30 29.0 -4.65655190431 0.061738939584
31 30.0 -4.71757978327 0.0603065587109
32 31.0 -4.77714481686 0.0588135679005
33 32.0 -4.83518737548 0.057261950911
34 33.0 -4.89164988211 0.0556538286799
35 34.0 -4.94647694795 0.0539914561312
36 35.0 -4.99961550465 0.0522772186102
37 36.0 -5.05101493277 0.0505136279528
38 37.0 -5.10062718621 0.048703318195
39 38.0 -5.14840691207 0.0468490409338
40 39.0 -5.19431156578 0.0449536603471
41 40.0 -5.23830152101 0.0430201478838
42 41.0 -5.28034017422 0.0410515766363
43 42.0 -5.3203940433 0.0390511154063
44 43.0 -5.35843286021 0.0370220224793
45 44.0 -5.39442965726 0.0349676391193
46 45.0 -5.4283608467 0.0328913828015
47 46.0 -5.46020629342 0.0307967401964
48 47.0 -5.48994938059 0.028687259923
49 48.0 -5.51757706789 0.0265665450883
50 49.0 -5.54307994213 0.0244382456298
51 50.0 -5.56645226024 0.0223060504811
52 51.0 -5.58769198425 0.0201736795783
53 52.0 -5.60680080825 0.0180448757265
54 53.0 -5.62378417713 0.0159233963481
55 54.0 -5.63865129702 0.0138130051308
56 55.0 -5.6514151374 0.0117174635982
57 56.0 -5.66209242462 0.00964052262251
58 57.0 -5.67070362704 0.00758591390103
59 58.0 -5.67727293157 0.00555734141841
60 59.0 -5.6818282117 0.00355847291538
61 60.0 -5.68440098698 0.00159293138608
62 61.0 -5.68502637408 -0.000335713374531
63 62.0 -5.68374302934 -0.00222395315148
64 63.0 -5.68059308309 -0.0040683495974
65 64.0 -5.67562206565 -0.00586554240548
66 65.0 -5.66887882528 -0.00761225734683
67 66.0 -5.66041543813 -0.00930531415106
68 67.0 -5.65028711044 -0.0109416342099
69 68.0 -5.63855207307 -0.0125182480831
70 69.0 -5.6252714687 -0.0140323027883
71 70.0 -5.61050923182 -0.0154810688529
72 71.0 -5.59433196178 -0.0168619471125
73 72.0 -5.57680878923 -0.0181724752358
74 73.0 -5.5580112361 -0.019410333958
75 74.0 -5.53801306959 -0.0205733530082
76 75.0 -5.51689015031 -0.0216595167121
77 76.0 -5.49472027505 -0.0226669692568
78 77.0 -5.47158301441 -0.0235940196022
79 78.0 -5.44755954575 -0.0244391460249
80 79.0 -5.42273248172 -0.0252010002837
81 80.0 -5.3971856949 -0.0258784113929
82 81.0 -5.37100413881 -0.0264703889936
83 82.0 -5.34427366574 -0.0269761263135
84 83.0 -5.31708084192 -0.0273950027051
85 84.0 -5.28951276022 -0.0277265857564
86 85.0 -5.26165685114 -0.0279706329651
87 86.0 -5.23360069216 -0.0281270929735
88 87.0 -5.20543181621 -0.0281961063563
89 88.0 -5.17723751951 -0.0281780059613
90 89.0 -5.14910466934 -0.0280733167983
91 90.0 -5.12111951208 -0.0278827554757
92 91.0 -5.09336748214 -0.0276072291861
93 92.0 -5.06593301201 -0.0272478342399
94 93.0 -5.0388993441 -0.026805854151
95 94.0 -5.01234834466 -0.0262827572773
96 95.0 -4.98636032033 -0.0256801940208
97 96.0 -4.96101383762 -0.0249999935924
98 97.0 -4.93638554598 -0.0242441603499
99 98.0 -4.91255000457 -0.0234148697145
100 99.0 -4.88957951348 -0.0225144636776
101 100.0 -4.86754394953 -0.0215454459053
102 101.0 -4.84651060724 -0.0205104764546
103 102.0 -4.8265440452 -0.01941236611
104 103.0 -4.80770593836 -0.0182540703564
105 104.0 -4.79005493648 -0.0170386830008
106 105.0 -4.77364652914 -0.0157694294583
107 106.0 -4.7585329176 -0.0144496597171
108 107.0 -4.74476289391 -0.0130828410011
109 108.0 -4.73238172744 -0.0116725501446
110 109.0 -4.72143105919 -0.0102224657007
111 110.0 -4.71194880414 -0.00873635979846
112 111.0 -4.70396906182 -0.0072180897712
113 112.0 -4.69752203541 -0.00567158957449
114 113.0 -4.69263395945 -0.00410086101469
115 114.0 -4.68932703648 -0.00250996480925
116 115.0 -4.68761938265 -0.000903011500147
117 116.0 -4.68752498248 0.00071584775762
118 117.0 -4.68905365291 0.00234243051027
119 118.0 -4.69221101668 0.00397253239976
120 119.0 -4.69699848518 0.00560193661579
121 120.0 -4.70341325069 0.00722642338265
122 121.0 -4.71144828821 0.00884177945771
123 122.0 -4.72109236669 0.0104438076188
124 123.0 -4.73233006984 0.0120283361174
125 124.0 -4.74514182625 0.0135912280748
126 125.0 -4.75950394898 0.0151283907985
127 126.0 -4.77538868431 0.0166357849963
128 127.0 -4.79276426974 0.0181094338658
129 128.0 -4.81159500092 0.0195454320375
130 129.0 -4.83184130754 0.0209399543498
131 130.0 -4.8534598378 0.0222892644342
132 131.0 -4.87640355143 0.0235897230915
133 132.0 -4.90062182095 0.0248377964369
134 133.0 -4.92606054096 0.0260300637961
135 134.0 -4.95266224518 0.0271632253326
136 135.0 -4.98036623096 0.028234109388
137 136.0 -5.00910869107 0.0292396795182
138 137.0 -5.03882285221 0.0301770412082
139 138.0 -5.06943912022 0.0310434482505
140 139.0 -5.10088523142 0.0318363087705
141 140.0 -5.13308640979 0.0325531908865
142 141.0 -5.16596552963 0.0331918279898
143 142.0 -5.19944328334 0.0337501236332
144 143.0 -5.23343835383 0.0342261560164
145 144.0 -5.26786759123 0.0346181820585
146 145.0 -5.30264619353 0.0349246410472
147 146.0 -5.33768789051 0.0351441578585
148 147.0 -5.37290513082 0.0352755457383
149 148.0 -5.40820927152 0.0353178086401
150 149.0 -5.4435107698 0.0352701431151
151 150.0 -5.4787193763 0.0351319397498
152 151.0 -5.51374432971 0.0349027841491
153 152.0 -5.54849455206 0.0345824574643
154 153.0 -5.58287884436 0.0341709364636
155 154.0 -5.61680608206 0.0336683931487
156 155.0 -5.65018540988 0.0330751939177
157 156.0 -5.68292643563 0.0323918982779
158 157.0 -5.71493942249 0.0316192571138
159 158.0 -5.74613547931 0.0307582105139
160 159.0 -5.77642674856 0.029809885165
161 160.0 -5.80572659147 0.0287755913197
162 161.0 -5.83394976986 0.0276568193473
163 162.0 -5.86101262442 0.0264552358763
164 163.0 -5.8868332488 0.025172679541
165 164.0 -5.91133165941 0.0238111563427
166 165.0 -5.93442996024 0.0223728346376
167 166.0 -5.95605250261 0.0208600397671
168 167.0 -5.97612603931 0.0192752483425
169 168.0 -5.99457987285 0.0176210822011
170 169.0 -6.01134599757 0.015900302049
171 170.0 -6.02635923519 0.014115800807
172 171.0 -6.03955736358 0.0122705966784
173 172.0 -6.05088123845 0.0103678259555
174 173.0 -6.0602749078 0.00841073558436
175 174.0 -6.06768571866 0.00640267550713
176 175.0 -6.0730644163 0.00434709080102
177 176.0 -6.07636523524 0.00224751363529
178 177.0 -6.07754598232 0.000107555066143
179 178.0 -6.07656811141 -0.00206910330914
180 179.0 -6.07339678973 -0.00427871781763
181 180.0 -6.06800095563 -0.00651749127408
182 181.0 -6.06035336781 -0.00878158162059
183 182.0 -6.05043064586 -0.0110671106207
184 183.0 -6.03821330204 -0.0133701725859
185 184.0 -6.02368576439 -0.0156868431131
186 185.0 -6.00683639108 -0.0180131878107
187 186.0 -5.98765747603 -0.0203452709919
188 187.0 -5.96614524589 -0.0226791643135
189 188.0 -5.94229984843 -0.025010955339
190 189.0 -5.91612533236 -0.0273367560054
191 190.0 -5.88762961878 -0.0296527109716
192 191.0 -5.85682446433 -0.0319550058299
193 192.0 -5.82372541626 -0.0342398751598
194 193.0 -5.78835175943 -0.0365036104045
195 194.0 -5.75072645562 -0.0387425675516
196 195.0 -5.71087607524 -0.0409531746008
197 196.0 -5.66883072166 -0.0431319387984
198 197.0 -5.62462394846 -0.0452754536249
199 198.0 -5.57829266983 -0.0473804055171
200 199.0 -5.5298770643 -0.0494435803104
201 200.0 -5.47942047235 -0.0514618693867
202 201.0 -5.42696928781 -0.0534322755136
203 202.0 -5.37257284377 -0.055351918363
204 203.0 -5.316283293 -0.0572180396955
205 204.0 -5.25815548345 -0.059028008202
206 205.0 -5.19824682901 -0.0607793239895
207 206.0 -5.13661717604 -0.0624696227052
208 207.0 -5.0733286659 -0.0640966792879
209 208.0 -5.00844559393 -0.0656584113417
210 209.0 -4.94203426529 -0.0671528821253
211 210.0 -4.87416284794 -0.0685783031513
212 211.0 -4.80490122327 -0.0699330363936
213 212.0 -4.7343208347 -0.0712155960973
214 213.0 -4.66249453466 -0.0724246501921
215 214.0 -4.58949643037 -0.0735590213066
216 215.0 -4.51540172879 -0.0746176873849
217 216.0 -4.44028658118 -0.0755997819067
218 217.0 -4.3642279276 -0.0765045937139
219 218.0 -4.28730334182 -0.0773315664459
220 219.0 -4.20959087694 -0.0780802975905
221 220.0 -4.13116891218 -0.0787505371538
222 221.0 -4.0521160012 -0.0793421859574
223 222.0 -3.97251072229 -0.0798552935693
224 223.0 -3.89243153076 -0.0802900558785
225 224.0 -3.81195661404 -0.0806468123209
226 225.0 -3.73116374964 -0.0809260427693
227 226.0 -3.65013016636 -0.0811283640964
228 227.0 -3.56893240921 -0.0812545264246
229 228.0 -3.48764620813 -0.0813054090744
230 229.0 -3.4063463509 -0.0812820162266
231 230.0 -3.32510656064 -0.0811854723104
232 231.0 -3.24399937793 -0.081017017134
233 232.0 -3.16309604794 -0.0807780007742
234 233.0 -3.08246641287 -0.0804698782381
235 234.0 -3.00217880976 -0.0800942039176
236 235.0 -2.92229997393 -0.079652625851
237 236.0 -2.84289494829 -0.0791468798106
238 237.0 -2.76402699866 -0.0785787832348
239 238.0 -2.68575753514 -0.0779502290223
240 239.0 -2.60814603984 -0.077263179207
241 240.0 -2.53125000097 -0.0765196585342
242 241.0 -2.4551248533 -0.0757217479546
243 242.0 -2.37982392531 -0.0748715780578
244 243.0 -2.30539839282 -0.073971322463
245 244.0 -2.23189723927 -0.0730231911866
246 245.0 -2.15936722267 -0.072029424007
247 246.0 -2.0878528491 -0.0709922838436
248 247.0 -2.01739635293 -0.0699140501714
249 248.0 -1.94803768347 -0.0687970124882
250 249.0 -1.87981449824 -0.0676434638537
251 250.0 -1.81276216256 -0.0664556945194
252 251.0 -1.74691375554 -0.0652359856651
253 252.0 -1.68230008218 -0.0639866032624
254 253.0 -1.61894969164 -0.0627097920793
255 254.0 -1.55688890134 -0.0614077698443
256 255.0 -1.49614182687 -0.0600827215855
257 256.0 -1.43673041741 -0.05873679416
258 257.0 -1.37867449659 -0.0573720909874
259 258.0 -1.32199180845 -0.0559906670036
260 259.0 -1.26669806833 -0.0545945238457
261 260.0 -1.21280701853 -0.0531856052829
262 261.0 -1.1603304883 -0.0517657929031
263 262.0 -1.1092784581 -0.0503369020679
264 263.0 -1.05965912771 -0.0489006781451
265 264.0 -1.01147898802 -0.0474587930279
266 265.0 -0.964742896092 -0.0460128419505
267 266.0 -0.919454153297 -0.0445643406057
268 267.0 -0.875614586172 -0.0431147225719
269 268.0 -0.833224629688 -0.0416653370554
270 269.0 -0.792283412613 -0.0402174469521
271 270.0 -0.752788844664 -0.038772227232
272 271.0 -0.714737705101 -0.0373307636499
273 272.0 -0.67812573245 -0.0358940517831
274 273.0 -0.642947715028 -0.0344629963972
275 274.0 -0.609197581934 -0.0330384111393
276 275.0 -0.576868494182 -0.0316210185584
277 276.0 -0.545952935658 -0.0302114504483
278 277.0 -0.51644280357 -0.0288102485125
279 278.0 -0.488329498068 -0.0274178653447
280 279.0 -0.461604010741 -0.0260346657211
281 280.0 -0.436257011655 -0.0246609281969
282 281.0 -0.412278934657 -0.023296847002
283 282.0 -0.389660060626 -0.0219425342253
284 283.0 -0.368390598407 -0.0205980222818
285 284.0 -0.348460763137 -0.01926326665
286 285.0 -0.329860851704 -0.0179381488715
287 286.0 -0.312581315078 -0.0166224797996
288 287.0 -0.296612827279 -0.015316003087
289 288.0 -0.281946350734 -0.0140183988977
290 289.0 -0.268573197826 -0.0127292878319
291 290.0 -0.256485088408 -0.0114482350481
292 291.0 -0.245674203109 -0.0101747545698
293 292.0 -0.236133232246 -0.00890831375923
294 293.0 -0.227855420178 -0.00764833794542
295 294.0 -0.220834604976 -0.00639421518813
296 295.0 -0.215065253253 -0.00514530116277
297 296.0 -0.210542490065 -0.00390092414876
298 297.0 -0.207262123775 -0.00266039010467
299 298.0 -0.205220665805 -0.00142298781263
300 299.0 -0.204415345223 -0.000187994074493
301 300.0 -0.204844118104 0.00104532105779
302 301.0 -0.206505671662 0.00227768903543
303 302.0 -0.209399423126 0.0035098375675
304 303.0 -0.213525513386 0.00474248539479
305 304.0 -0.218884795423 0.00597633710062
306 305.0 -0.225478817581 0.00721207797616
307 306.0 -0.233309801737 0.00845036895769
308 307.0 -0.242380616448 0.00969184165314
309 308.0 -0.252694745185 0.0109370934746
310 309.0 -0.264256249747 0.0121866828936
311 310.0 -0.277069729013 0.0134411248358
312 311.0 -0.291140273151 0.0147008862297
313 312.0 -0.306473413467 0.0159663817261
314 313.0 -0.323075068066 0.0172379696031
315 314.0 -0.340951483513 0.018515947869
316 315.0 -0.360109172702 0.0198005505798
317 316.0 -0.380554849155 0.0210919443819
318 317.0 -0.402295357987 0.0223902252933
319 318.0 -0.425337603767 0.0236954157356
320 319.0 -0.449688475549 0.0250074618263
321 320.0 -0.475354769327 0.0263262309427
322 321.0 -0.50234310819 0.0276515095659
323 322.0 -0.530659860472 0.0289830014145
324 323.0 -0.560311056174 0.0303203258736
325 324.0 -0.59130230198 0.0316630167284
326 325.0 -0.623638695141 0.0330105212056
327 326.0 -0.657324736579 0.0343621993296
328 327.0 -0.692364243488 0.0357173235955
329 328.0 -0.728760261774 0.0370750789637
330 329.0 -0.766514978659 0.0384345631765
331 330.0 -0.805629635748 0.0397947873984
332 331.0 -0.846104442913 0.04115467718
333 332.0 -0.887938493289 0.042513073745
334 333.0 -0.93112967973 0.0438687355968
335 334.0 -0.975674613021 0.0452203404434
336 335.0 -1.02156854218 0.0465664874361
337 336.0 -1.06880527714 0.0479056997168
338 337.0 -1.11737711415 0.0492364272675
339 338.0 -1.16727476416 0.0505570500574
340 339.0 -1.2184872845 0.051865881477
341 340.0 -1.27100201415 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

19
tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/run.in.min
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@ -1,19 +0,0 @@
# -- 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

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