forked from lijiext/lammps
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This commit is contained in:
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@ -38,7 +38,7 @@ if "${eng} > ${eng_previous}" then "jump file1" else "jump file2"
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</PRE>
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||||
<P><B>Description:</B>
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</P>
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||||
<P>This command provides an in-then-else capability within an input
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<P>This command provides an if-then-else capability within an input
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||||
script. A Boolean expression is evaluted and the result is TRUE or
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||||
FALSE. Note that as in the examples above, the expression can contain
|
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variables, as defined by the <A HREF = "variable.html">variable</A> command, which
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@ -51,7 +51,7 @@ commands (t1, t2, ..., tN) are executed. If it is FALSE, then Boolean
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expressions associated with successive elif keywords are evaluated
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until one is found to be true, in which case its commands (f1, f2,
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..., fN) are executed. If no Boolean expression is TRUE, then the
|
||||
commands associated witht the else keyword, namely (e1, e2, ..., eN),
|
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commands associated with the else keyword, namely (e1, e2, ..., eN),
|
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are executed. The elif and else keywords and their associated
|
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commands are optional. If they aren't specified and the initial
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Boolean expression is FALSE, then no commands are executed.
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|
|
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|||
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@ -35,7 +35,7 @@ if "$\{eng\} > $\{eng_previous\}" then "jump file1" else "jump file2" :pre
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[Description:]
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||||
|
||||
This command provides an in-then-else capability within an input
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||||
This command provides an if-then-else capability within an input
|
||||
script. A Boolean expression is evaluted and the result is TRUE or
|
||||
FALSE. Note that as in the examples above, the expression can contain
|
||||
variables, as defined by the "variable"_variable.html command, which
|
||||
|
|
@ -48,7 +48,7 @@ commands (t1, t2, ..., tN) are executed. If it is FALSE, then Boolean
|
|||
expressions associated with successive elif keywords are evaluated
|
||||
until one is found to be true, in which case its commands (f1, f2,
|
||||
..., fN) are executed. If no Boolean expression is TRUE, then the
|
||||
commands associated witht the else keyword, namely (e1, e2, ..., eN),
|
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commands associated with the else keyword, namely (e1, e2, ..., eN),
|
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are executed. The elif and else keywords and their associated
|
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commands are optional. If they aren't specified and the initial
|
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Boolean expression is FALSE, then no commands are executed.
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|
|
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@ -0,0 +1,28 @@
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Author: Andrew Jewett, Shea Group, http://www.chem.ucsb.edu/~sheagroup/
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Copyright (c) 2013, Regents of the University of California
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All rights reserved.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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||||
* 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.
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* 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.
|
||||
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||||
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
|
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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
|
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INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
|
||||
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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||||
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
|
||||
THE POSSIBILITY OF SUCH DAMAGE.
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|
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@ -0,0 +1,61 @@
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-- Description: --
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Moltemplate is a cross-platform text-based molecule builder for LAMMPS.
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-- Typical usage: --
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moltemplate.sh [-atomstyle style] [-pdb/-xyz coord_file] file.lt
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-- Web page: --
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Documentation, examples, and supporting code can be downloaded at:
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http://www.moltemplate.org
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The most up-to-date version of moltemplate can be downloaded here.
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(After download, you can unpack the archive using:
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tar xzf moltemplate_2012-3-31.tar.gz
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The date will vary from version to version.)
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----------------------------------------------------
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---------- INSTALLATION INSTRUCTIONS: ------------
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----------------------------------------------------
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This directory should contain two folders:
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src/ <-- location of all python and bash scripts
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common/ <-- location of shared force fields and molecules
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The ``moltemplate.sh'' script and the python scripts that it invokes are
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located in the ``src/'' subdirectory. You should update your PATH environment
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variable to include this directory.
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If you do not know what a PATH environment variable is, read:
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http://www.linfo.org/path_env_var.html
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(I receive this question often.)
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It is also a good idea to set your MOLTEMPLATE_PATH environment variable to
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point to the ``common/'' subdirectory.
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(Force fields and commonly used molecules will eventually be located here.)
|
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|
||||
-- Installation example ---
|
||||
|
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Suppose the directory with this README.TXT file is located at ~/moltemplate.
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|
||||
If you use the bash shell, typically you would edit your
|
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~/.profile, ~/.bash_profile or ~/.bashrc files to contain the following lines:
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export PATH="$PATH:$HOME/moltemplate/src"
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export MOLTEMPLATE_PATH="$HOME/moltemplate/common"
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If you use the tcsh shell, typically you would edit your
|
||||
~/.login, ~/.cshrc, or ~/.tcshrc files to contain the following lines:
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setenv PATH "$PATH:$HOME/moltemplate/src"
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setenv MOLTEMPLATE_PATH "$HOME/moltemplate/common"
|
||||
|
||||
-- Requirements: --
|
||||
|
||||
Moltemplate requires the Bourne-shell, and a recent version of python
|
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(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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@ -0,0 +1,106 @@
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# This file contains a unit cell for building graphene and nanotubes
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#
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#
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# The 2AtomCellAlignX "molecule" defined below is a minimal unit cell for any
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# hexagonal tesselation in 2-dimensions. (See "graphene_unit_cell.jpg")
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# Surfaces constructed with this unit cell can be flat or curved into tubes.
|
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# The distance between nearest-neighbor carbon atoms (ie the length of a
|
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# carbon-carbon bond) is equal to "d" which I set to 1.420 Angstroms.
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#
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# d = length of each hexagon's side = 1.42 Angstroms
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# L = length of each hexagon = 2*d = 2.84 Angstroms
|
||||
# W = width of each hexagon = 2*d*sqrt(3)/2 = 2.4595121467478056 Angstroms
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#
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||||
# Consequently, the Lattice-cell vectors for singe-layer graphene are:
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# (2.4595121467478, 0, 0) (aligned with X axis)
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# (1.2297560733739, 2.13, 0) (2.13 = 1.5*d)
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# So, to build a sheet of graphite, you could use:
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# sheet = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0)
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# [10].move(1.2297560733739,2.13,0)
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Graphene {
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2AtomCellAlignX
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{
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||||
# atomID molID atomType charge x y z
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write("Data Atoms") {
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$atom:C1 $mol:... @atom:../C 0.0 -0.61487803668695 -0.355 0.0
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||||
$atom:C2 $mol:... @atom:../C 0.0 0.61487803668695 0.355 0.0
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||||
}
|
||||
}
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||||
|
||||
# Now define properties of the Carbon graphene atom
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||||
|
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write_once("In Init") {
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pair_style hybrid lj/charmm/coul/charmm 9.0 10.0
|
||||
}
|
||||
|
||||
write_once("Data Masses") {
|
||||
@atom:C 12.0
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}
|
||||
|
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write_once("In Settings") {
|
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# i j epsilon sigma
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pair_coeff @atom:C @atom:C lj/charmm/coul/charmm 0.068443 3.407
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||||
|
||||
# These Lennard-Jones parameters come from
|
||||
# R. Saito, R. Matsuo, T. Kimura, G. Dresselhaus, M.S. Dresselhaus,
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# Chem Phys Lett, 348:187 (2001)
|
||||
|
||||
# Define a group consisting of only carbon atoms in graphene molecules
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group Cgraphene type @atom:C
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}
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||||
|
||||
# Notice that the two atoms in the unit-cell above lie in the XY plane.
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# (Their z-coordinate is zero). It's also useful to have a version of
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# this object which lies in the XZ plan. So we define this below:
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2AtomCellAlignXZ = 2AtomCellAlignX.rot(90,1,0,0)
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||||
|
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} # Graphene
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||||
|
||||
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||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
# ------------ Graphite -----------
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||||
#
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# Note: For graphite: sheets stacked in the Z direction are separated by a
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# distance of 3.35 Angstroms, and shifted in an alternating +/-Y direction
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||||
# by a distance of d (1.42 Angstroms). To add additional graphene layers
|
||||
# you could use:
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||||
# sheet2 = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0)
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||||
# [10].move(1.2297560733739,2.13,0)
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||||
# sheet2[*][*].move(0, 1.42, 3.35)
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# sheet3 = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0)
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# [10].move(1.2297560733739,2.13,0)
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# sheet3[*][*].move(0, -1.42, 6.70)
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# etc...
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||||
# However, to build a thick sheet of graphite, it would
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# be more efficient to use a 4-atom unit cell:
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#
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#Graphene {
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# GraphiteCell {
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# # atomID molID atomType charge x y z
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# write("Data Atoms") {
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# $atom:C1 $mol:... @atom:../C 0.0 -0.61487803668695 -0.355 0.0
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||||
# $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
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||||
# $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:
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||||
#
|
||||
# graphite = new Graphene/GraphiteCell [10].move(2.4595121467478,0,0)
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||||
# [10].move(1.2297560733739,2.13,0)
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||||
# [5].move(0,0,6.70)
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Binary file not shown.
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After Width: | Height: | Size: 13 KiB |
Binary file not shown.
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After Width: | Height: | Size: 21 KiB |
Binary file not shown.
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After Width: | Height: | Size: 5.5 KiB |
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@ -0,0 +1,52 @@
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|||
# file "spce.lt"
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||||
#
|
||||
# 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
|
||||
|
||||
|
|
@ -0,0 +1,57 @@
|
|||
# This ice (1h) unit cell is rectangular and contains 8 water molecules.
|
||||
# (Coordinates and cell dimensions converted were from a PDB file.)
|
||||
# The dimensions of the unit cell (in Angstroms) are: 4.521 7.832 7.362
|
||||
|
||||
|
||||
import "spce.lt" # <-- define the "SPCE" molecule
|
||||
|
||||
SpceIceRect8 {
|
||||
|
||||
# Create a 3-dimensional array of 8 water molecules
|
||||
|
||||
wat = new SPCE[2][2][2]
|
||||
|
||||
# Array indices will be correlated with position [xindex][yindex][zindex]
|
||||
|
||||
# You can overwrite coordinates of atoms after they were created this way:
|
||||
# (Order is not important)
|
||||
# atom-ID molecule-ID atomType charge newX newY newZ
|
||||
|
||||
write("Data Atoms") {
|
||||
$atom:wat[1][0][0]/O $mol:wat[1][0][0] @atom:SPCE/O -0.8476 3.391 1.305 1.381
|
||||
$atom:wat[1][0][0]/H1 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 3.391 0.370 1.710
|
||||
$atom:wat[1][0][0]/H2 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 2.582 1.772 1.710
|
||||
$atom:wat[1][0][1]/O $mol:wat[1][0][1] @atom:SPCE/O -0.8476 3.391 1.305 5.981
|
||||
$atom:wat[1][0][1]/H1 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 3.391 1.305 6.970
|
||||
$atom:wat[1][0][1]/H2 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 4.200 1.772 5.652
|
||||
$atom:wat[0][0][0]/O $mol:wat[0][0][0] @atom:SPCE/O -0.8476 1.131 2.611 2.300
|
||||
$atom:wat[0][0][0]/H1 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 1.131 2.611 3.289
|
||||
$atom:wat[0][0][0]/H2 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 0.320 2.143 1.971
|
||||
$atom:wat[0][0][1]/O $mol:wat[0][0][1] @atom:SPCE/O -0.8476 1.131 2.611 5.061
|
||||
$atom:wat[0][0][1]/H1 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.940 2.143 5.391
|
||||
$atom:wat[0][0][1]/H2 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.131 3.546 5.391
|
||||
$atom:wat[0][1][0]/O $mol:wat[0][1][0] @atom:SPCE/O -0.8476 1.131 5.221 1.381
|
||||
$atom:wat[0][1][0]/H1 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.131 4.286 1.710
|
||||
$atom:wat[0][1][0]/H2 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 0.320 5.688 1.710
|
||||
$atom:wat[0][1][1]/O $mol:wat[0][1][1] @atom:SPCE/O -0.8476 1.131 5.221 5.981
|
||||
$atom:wat[0][1][1]/H1 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.131 5.221 6.970
|
||||
$atom:wat[0][1][1]/H2 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.940 5.688 5.652
|
||||
$atom:wat[1][1][0]/O $mol:wat[1][1][0] @atom:SPCE/O -0.8476 3.391 6.526 2.300
|
||||
$atom:wat[1][1][0]/H1 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 3.391 6.526 3.289
|
||||
$atom:wat[1][1][0]/H2 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 2.582 6.058 1.971
|
||||
$atom:wat[1][1][1]/O $mol:wat[1][1][1] @atom:SPCE/O -0.8476 3.391 6.526 5.061
|
||||
$atom:wat[1][1][1]/H1 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 4.200 6.058 5.391
|
||||
$atom:wat[1][1][1]/H2 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 3.391 7.462 5.391
|
||||
}
|
||||
} # IceRect8
|
||||
|
||||
# Credit goes to Martin Chaplin.
|
||||
# These coordinates were orignally downloaded from Martin Chaplin's
|
||||
# website: http://www.btinternet.com/~martin.chaplin/ice1h.html
|
||||
# ... and then they were stretched independently in the xy and z
|
||||
# directions in order to match the lattice parameters measured by
|
||||
# Rottger et al.,
|
||||
# "Lattice constants and thermal expansion of H2O and D2O ice Ih"
|
||||
# between 10 and 265K", Acta Crystallogr. B, 50 (1994) 644-648
|
||||
# I am using the lattice constants measured at temperature 265K
|
||||
# (and pressure=100Torr).
|
||||
|
|
@ -0,0 +1,13 @@
|
|||
This directory contains two LT files corresponding to
|
||||
different versions of TIP3P:
|
||||
|
||||
tip3pcharmm.lt # The implementation of TIP3P used by CHARMM (I think).
|
||||
tip3p2004.lt # The newer Price & Brooks, J. Chem Phys 2004 model
|
||||
# which uses long-range coulombics
|
||||
|
||||
I have not tested these files so I moved them here.
|
||||
(If you have tested these files, and they work, or if you have other comments
|
||||
or suggestions, feel free to email me at jewett.aij at gmail dot com.)
|
||||
|
||||
Andrew
|
||||
2012-10-20
|
||||
|
|
@ -0,0 +1,88 @@
|
|||
# file "tip3p2004.lt"
|
||||
#
|
||||
# H1 H2
|
||||
# \ /
|
||||
# O
|
||||
#
|
||||
# I think this is the TIP3P water described in the paper by
|
||||
# Daniel J. Price and Charles L. Brooks III
|
||||
# J. Chem. Phys., 121(20): 10096 (2004)
|
||||
# Specifically I think it refers to the "Model B" version of long-range TIP3P
|
||||
# described in the 3rd-to-last column of "Table I", on p.10099.
|
||||
|
||||
TIP3P2004 {
|
||||
|
||||
write_once("In Init") {
|
||||
# -- Default styles (for solo "TIP3P2004" water) --
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style hybrid lj/charmm/coul/long 10.0 10.5 10.5
|
||||
bond_style hybrid harmonic
|
||||
angle_style hybrid harmonic
|
||||
kspace_style pppm 0.0001
|
||||
pair_modify mix arithmetic
|
||||
}
|
||||
|
||||
write("Data Atoms") {
|
||||
$atom:O $mol:. @atom:O -0.830 0.0000000 0.00000 0.000000
|
||||
$atom:H1 $mol:. @atom:H 0.415 0.756950327 0.00000 0.5858822766
|
||||
$atom:H2 $mol:. @atom:H 0.415 -0.756950327 0.00000 0.5858822766
|
||||
}
|
||||
|
||||
write_once("Data Masses") {
|
||||
@atom:O 15.9994
|
||||
@atom:H 1.008
|
||||
}
|
||||
|
||||
write("Data Bonds") {
|
||||
$bond:OH1 @bond:OH $atom:O $atom:H1
|
||||
$bond:OH2 @bond:OH $atom:O $atom:H2
|
||||
}
|
||||
|
||||
write("Data Angles") {
|
||||
$angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
bond_coeff @bond:OH harmonic 450.0 0.9572
|
||||
angle_coeff @angle:HOH harmonic 55.0 104.52
|
||||
|
||||
#########################################################################
|
||||
#### There are two choices for for the O-O interactions
|
||||
#########################################################################
|
||||
#### O-O nonbonded interactions
|
||||
# For the 1983 Jorgensen version of TIP3P use:
|
||||
# pair_coeff @atom:O @atom:O lj/charmm/coul/charmm 0.1521 3.1507
|
||||
# For the 2004 Price & Brooks version of TIP3P use:
|
||||
pair_coeff @atom:O @atom:O lj/charmm/coul/charmm 0.102 3.188
|
||||
#########################################################################
|
||||
#### There are three choices for for the O-H and H-H interactions
|
||||
#########################################################################
|
||||
#### 1) CHARMM uses an arithmetic mixing-rule for the O-H sigma parameter
|
||||
pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.0460 0.4000
|
||||
pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.7753 #arithmetic
|
||||
#########################################################################
|
||||
#### 2) OPLS-AA uses geometric a mixing-fule for the O-H sigma parameter,
|
||||
#### If you want to use this, uncomment the following two lines:
|
||||
# pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.0460 0.4000
|
||||
# pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.1226 #geometric
|
||||
#########################################################################
|
||||
#### 3) The original Jorgensen 1983 parameterization has no OH or HH
|
||||
# lennard-jones interactions. For this behavior, uncomment these lines:
|
||||
# pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.00 0.4000
|
||||
# pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.00 1.7753
|
||||
#########################################################################
|
||||
|
||||
# Define a group for the tip3p water molecules:
|
||||
group tip3p type @atom:O @atom:H
|
||||
|
||||
# Optional: Constrain the angles and distances.
|
||||
# (Most implementations use this, but it is optional.)
|
||||
fix fSHAKE tip3p shake 0.0001 10 100 b @bond:OH a @angle:HOH
|
||||
# (Remember to "unfix" fSHAKE during minimization.)
|
||||
|
||||
}
|
||||
|
||||
} # "TIP3P2004" water molecule type
|
||||
|
||||
|
|
@ -0,0 +1,91 @@
|
|||
# file "tip3p_charmm.lt"
|
||||
#
|
||||
# H1 H2
|
||||
# \ /
|
||||
# O
|
||||
#
|
||||
# I think this is the TIP3P water model used by CHARMM (and probably AMBER)
|
||||
# It is (mostly) based on this paper:
|
||||
# Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem Phys, 79, 926 (1983)
|
||||
|
||||
TIP3Pcharmm {
|
||||
|
||||
write_once("In Init") {
|
||||
# -- Default styles (for solo "TIP3Pcharmm" water) --
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
# I'm not sure exactly which cutoffs distances are traditionally used in
|
||||
# the TIP3P water model used by CHARMM.
|
||||
# (See the Price JCP 2004 paper for a review.)
|
||||
# pair_style hybrid lj/charmm/coul/charmm 7.5 8.0 10.0 10.5
|
||||
# Try this instead:
|
||||
pair_style hybrid lj/charmm/coul/charmm 10.0 10.5 10.0 10.5
|
||||
|
||||
bond_style hybrid harmonic
|
||||
angle_style hybrid harmonic
|
||||
pair_modify mix arithmetic
|
||||
}
|
||||
|
||||
write("Data Atoms") {
|
||||
$atom:O $mol:. @atom:O -0.834 0.0000000 0.00000 0.000000
|
||||
$atom:H1 $mol:. @atom:H 0.417 0.756950327 0.00000 0.5858822766
|
||||
$atom:H2 $mol:. @atom:H 0.417 -0.756950327 0.00000 0.5858822766
|
||||
}
|
||||
|
||||
write_once("Data Masses") {
|
||||
@atom:O 15.9994
|
||||
@atom:H 1.008
|
||||
}
|
||||
|
||||
write("Data Bonds") {
|
||||
$bond:OH1 @bond:OH $atom:O $atom:H1
|
||||
$bond:OH2 @bond:OH $atom:O $atom:H2
|
||||
}
|
||||
|
||||
write("Data Angles") {
|
||||
$angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
bond_coeff @bond:OH harmonic 450.0 0.9572
|
||||
angle_coeff @angle:HOH harmonic 55.0 104.52
|
||||
|
||||
#########################################################################
|
||||
#### There are two choices for for the O-O interactions
|
||||
#########################################################################
|
||||
#### O-O nonbonded interactions
|
||||
# For the 1983 Jorgensen version of TIP3P use:
|
||||
pair_coeff @atom:O @atom:O lj/charmm/coul/charmm 0.1521 3.1507
|
||||
# For the 2004 Price & Brooks version of TIP3P use:
|
||||
# pair_coeff @atom:O @atom:O lj/charmm/coul/charmm 0.102 3.188
|
||||
#########################################################################
|
||||
#### There are three choices for for the O-H and H-H interactions
|
||||
#########################################################################
|
||||
#### 1) CHARMM uses an arithmetic mixing-rule for the O-H sigma parameter
|
||||
pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.0460 0.4000
|
||||
pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.7753 #arithmetic
|
||||
#########################################################################
|
||||
#### 2) OPLS-AA uses geometric a mixing-fule for the O-H sigma parameter,
|
||||
#### If you want to use this, uncomment the following two lines:
|
||||
# pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.0460 0.4000
|
||||
# pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.1226 #geometric
|
||||
#########################################################################
|
||||
#### 3) The original Jorgensen 1983 parameterization has no OH or HH
|
||||
# lennard-jones interactions. For this behavior, uncomment these lines:
|
||||
# pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.00 0.4000
|
||||
# pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.00 1.7753
|
||||
#########################################################################
|
||||
|
||||
# Define a group for the tip3p water molecules:
|
||||
group tip3p type @atom:O @atom:H
|
||||
|
||||
# Optional: Constrain the angles and distances.
|
||||
# (Most implementations use this, but it is optional.)
|
||||
fix fSHAKE tip3p shake 0.0001 10 100 b @bond:OH a @angle:HOH
|
||||
# (Remember to "unfix" fSHAKE during minimization.)
|
||||
|
||||
}
|
||||
|
||||
} # "TIP3Pcharmm" water molecule type
|
||||
|
||||
|
|
@ -0,0 +1,50 @@
|
|||
# This file stores complete LAMMPS data for the TraPPE model of saturated
|
||||
# hydrocarbon chains. In this "united-atom" model, each methyl group is
|
||||
# represented by a single atom. Forces between "atoms" are taken from the
|
||||
# TraPPE force-field. (J Phys Chem B, 1998, volume 102, pp.2569-2577)
|
||||
|
||||
TraPPE {
|
||||
|
||||
write_once("In Init") {
|
||||
# -- Default styles for "TraPPE" --
|
||||
units real
|
||||
atom_style full
|
||||
# (Hybrid force field styles were used for portability.)
|
||||
bond_style hybrid harmonic
|
||||
angle_style hybrid harmonic
|
||||
dihedral_style hybrid opls
|
||||
improper_style none
|
||||
pair_style hybrid lj/charmm/coul/charmm 9.0 11.0 9.0 11.0
|
||||
pair_modify mix arithmetic
|
||||
special_bonds lj 0.0 0.0 0.0
|
||||
}
|
||||
|
||||
write_once("Data Masses") {
|
||||
@atom:CH2 14.1707
|
||||
@atom:CH3 15.2507
|
||||
@atom:CH4 16.3307
|
||||
}
|
||||
|
||||
write_once("Data Angles By Type") {
|
||||
@angle:backbone @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated
|
||||
}
|
||||
|
||||
write_once("Data Dihedrals By Type") {
|
||||
@dihedral:backbone @atom:CH? @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated @bond:saturated
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
pair_coeff @atom:CH2 @atom:CH2 lj/charmm/coul/charmm 0.091411522 3.95
|
||||
pair_coeff @atom:CH3 @atom:CH3 lj/charmm/coul/charmm 0.194746286 3.75
|
||||
pair_coeff @atom:CH4 @atom:CH4 lj/charmm/coul/charmm 0.294106636 3.73
|
||||
bond_coeff @bond:saturated harmonic 120.0 1.54
|
||||
angle_coeff @angle:backbone harmonic 62.0022 114
|
||||
dihedral_coeff @dihedral:backbone opls 1.411036 -0.271016 3.145034 0.0
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
group TraPPE type @atom:CH2 @atom:CH3 @atom:CH4
|
||||
}
|
||||
|
||||
} # class TraPPE
|
||||
|
||||
|
|
@ -0,0 +1,54 @@
|
|||
# This file stores LAMMPS data for the "mW" water model.
|
||||
# (Molinero, V. and Moore, E.B., J. Phys. Chem. B 2009, 113, 4008-4016)
|
||||
#
|
||||
# In this model, each water molecule is represented by a single "mW" particle.
|
||||
# These particles interact with their neighbors via 3-body Stillinger-Weber
|
||||
# forces whose parameters are tuned to mimic directional hydrogen-bonding
|
||||
# in liquid water (as well as hexagonal ice, type II ice, and
|
||||
# low-density super-cooled liquid/amorphous water phases).
|
||||
|
||||
WatMW {
|
||||
write("Data Atoms") {
|
||||
$atom:mW $mol:. @atom:mW 0.0 0.0 0.0 0.0
|
||||
}
|
||||
|
||||
write_once("Data Masses") {
|
||||
@atom:mW 18.02
|
||||
}
|
||||
|
||||
write_once("system.in.sw") {
|
||||
mW mW mW 6.189 2.3925 1.8 23.15 1.2 -0.333333333 7.049556277 0.602224558 4 0 0
|
||||
}
|
||||
|
||||
write_once("In Init") {
|
||||
# -- Default styles for "WatMW" --
|
||||
units real
|
||||
pair_style sw
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
# --Now indicate which atom type(s) are simulated using the "sw" pair style
|
||||
# -- In this case only one of the atom types is used (the mW water "atom").
|
||||
|
||||
pair_coeff * * sw system.in.sw mW NULL NULL NULL
|
||||
|
||||
# -- Unfortunately LAMMPS itself does not understand molemlate syntax, so
|
||||
# -- the atoms are identified by order in the list, not by name. (The "mW"
|
||||
# -- refers to to an identifier in the system.in.sw file, not watmw.lt.)
|
||||
# -- This command says that the first atom type corresponds to the "mW"
|
||||
# -- atom in system.in.sw, and to ignore the remaining three atom types
|
||||
# -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt.
|
||||
# -- We don't want to use the "sw" force field for interactions involving
|
||||
# -- these atom types, so we put "NULL" there.)
|
||||
# -- Note: For this to work, you should probably run moltemplate this way:
|
||||
# -- moltemplate.sh -a "@atom:WatMW/mW 1" system.lt
|
||||
# -- This assigns the atom type named @atom:WatMW/mW to 1 (the first atom)
|
||||
}
|
||||
|
||||
# -- optional --
|
||||
|
||||
write_once("In Settings") {
|
||||
group WatMW type @atom:mW #(Atoms of this type belong to the "WatMW" group)
|
||||
}
|
||||
|
||||
} # WatMW
|
||||
|
|
@ -0,0 +1,70 @@
|
|||
This example shows how to put a protein (inclusion) in a
|
||||
lipid bilayer mixture composed of two different lipids (DPPC and DLPC).
|
||||
The DPPC lipid model is described here:
|
||||
G. Brannigan, P.F. Philips, and F.L.H. Brown,
|
||||
Physical Review E, Vol 72, 011915 (2005)
|
||||
(The DLPC model is a truncated version of DPPC. Modifications discussed below.)
|
||||
The protein model is described here:
|
||||
G. Bellesia, AI Jewett, and J-E Shea,
|
||||
Protein Science, Vol19 141-154 (2010)
|
||||
|
||||
--- PREREQUISITES: ---
|
||||
|
||||
1) This example requires the "dihedral_style fourier", which is currently
|
||||
in the USER-MISC package. Build LAMMPS with this package enabled using
|
||||
make yes-user-misc
|
||||
before compiling LAMMPS.
|
||||
(See http://lammps.sandia.gov/doc/Section_start.html#start_3 for details.)
|
||||
|
||||
2) This example may require additional features to be added to LAMMPS.
|
||||
If LAMMPS complains about an "Invalid pair_style", then
|
||||
a) download the "additional_lammps_code" from
|
||||
http://moltemplate.org (upper-left corner menu)
|
||||
b) unpack it
|
||||
c) copy the .cpp and .h files to the src folding of your lammps installation.
|
||||
d) (re)compile LAMMPS.
|
||||
|
||||
|
||||
----- Details --------
|
||||
|
||||
This example contains a coarse-grained model of a 4-helix bundle protein
|
||||
inserted into a lipid bilayer (made from a mixture of DPPC and DLPC).
|
||||
|
||||
-- Protein Model: --
|
||||
|
||||
The coarse-grained protein is described in:
|
||||
G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010)
|
||||
Here we use the "AUF2" model described in that paper.
|
||||
(The hydrophobic beads face outwards.)
|
||||
|
||||
-- Memebrane Model: --
|
||||
|
||||
The DPPC lipid bilayer described in:
|
||||
G. Brannigan, P.F. Philips, and F.L.H. Brown,
|
||||
Physical Review E, Vol 72, 011915 (2005)
|
||||
and:
|
||||
M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown
|
||||
J. Chem. Phys. 135, 244701 (2011)
|
||||
|
||||
As in Watson(JCP 2011), rigid bond-length constraints
|
||||
have been replaced by harmonic bonds.
|
||||
|
||||
A truncated version of this lipid (named "DLPC") has also been added.
|
||||
The bending stiffness of each lipid has been increased to compensate
|
||||
for the additional disorder resulting from mixing two different types
|
||||
of lipids together. (Otherwise pores appear.)
|
||||
Unlike the original "DPPC" molecule model, the new "DPPC" and "DLPC" models
|
||||
have not been carefully parameterized to reproduce the correct behavior in
|
||||
a lipid bilayer mixture.
|
||||
|
||||
|
||||
-------------
|
||||
|
||||
Instructions on how to build LAMMPS input files and
|
||||
run a short simulation are provided in other README files.
|
||||
|
||||
step 1)
|
||||
README_setup.sh
|
||||
|
||||
step2)
|
||||
README_run.sh
|
||||
|
|
@ -0,0 +1,33 @@
|
|||
# --- Running LAMMPS ---
|
||||
# -- Prerequisites: --
|
||||
# The "run.in.nvt" file is a LAMMPS input script containing
|
||||
# references to the input scripts and data files
|
||||
# you hopefully have created earlier with moltemplate.sh:
|
||||
# system.in.init, system.in.settings, system.data, and table_int.dat
|
||||
# If not, carry out the instructions in "README_setup.sh".
|
||||
#
|
||||
# -- Instructions: --
|
||||
# If "lmp_linux" is the name of the command you use to invoke lammps,
|
||||
# then you would run lammps on these files this way:
|
||||
|
||||
|
||||
lmp_linux -i run.in.npt # Run a simulation at constant pressure (tension)
|
||||
|
||||
#or
|
||||
|
||||
lmp_linux -i run.in.nvt # Run a simulation at constant volume
|
||||
|
||||
#(Note: The constant volume simulation lacks pressure equilibration. These are
|
||||
# completely separate simulations. The results of the constant pressure
|
||||
# simulation are ignored when beginning the simulation at constant volume.
|
||||
# This can be fixed. Read "run.in.nvt" for equilibration instructions.)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
# If you have compiled the MPI version of lammps, you can run lammps in parallel
|
||||
#mpirun -np 4 lmp_linux -i run.in.npt
|
||||
#or
|
||||
#mpirun -np 4 lmp_linux -i run.in.nvt
|
||||
# (assuming you have 4 processors available)
|
||||
|
|
@ -0,0 +1,28 @@
|
|||
# Use these commands to generate the LAMMPS input script and data file
|
||||
# (and other auxilliary files):
|
||||
|
||||
|
||||
# Create LAMMPS input files this way:
|
||||
cd moltemplate_files
|
||||
|
||||
# run moltemplate
|
||||
|
||||
moltemplate.sh system.lt
|
||||
|
||||
# This will generate various files with names ending in *.in* and *.data.
|
||||
# These files are the input files directly read by LAMMPS. Move them to
|
||||
# the parent directory (or wherever you plan to run the simulation).
|
||||
|
||||
mv -f system.in* system.data ../
|
||||
|
||||
# The "table_int.dat" file contains tabular data for the lipid INT-INT atom
|
||||
# 1/r^2 interaction. We need it too. (This slows down the simulation by x2,
|
||||
# so I might look for a way to get rid of it later.)
|
||||
cp -f table_int.dat ../
|
||||
|
||||
# Optional:
|
||||
# The "./output_ttree/" directory is full of temporary files generated by
|
||||
# moltemplate. They can be useful for debugging, but are usually thrown away.
|
||||
rm -rf output_ttree/
|
||||
|
||||
cd ../
|
||||
|
|
@ -0,0 +1,87 @@
|
|||
|
||||
------- To view a lammps trajectory in VMD --------
|
||||
|
||||
|
||||
1) Build a PSF file for use in viewing with VMD.
|
||||
|
||||
This step works with VMD 1.9 and topotools 1.2.
|
||||
(Older versions, like VMD 1.8.6, don't support this.)
|
||||
|
||||
|
||||
a) Start VMD
|
||||
b) Menu Extensions->Tk Console
|
||||
c) Enter:
|
||||
|
||||
(I assume that the the DATA file is called "system.data")
|
||||
|
||||
topo readlammpsdata system.data full
|
||||
animate write psf system.psf
|
||||
|
||||
2)
|
||||
|
||||
Later, to Load a trajectory in VMD:
|
||||
|
||||
Start VMD
|
||||
Select menu: File->New Molecule
|
||||
-Browse to select the PSF file you created above, and load it.
|
||||
(Don't close the window yet.)
|
||||
-Browse to select the trajectory file.
|
||||
If necessary, for "file type" select: "LAMMPS Trajectory"
|
||||
Load it.
|
||||
|
||||
---- A note on trajectory format: -----
|
||||
If the trajectory is a DUMP file, then make sure the it contains the
|
||||
information you need for pbctools (see below. I've been using this
|
||||
command in my LAMMPS scripts to create the trajectories:
|
||||
|
||||
dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
|
||||
|
||||
It's a good idea to use an atom_style which supports molecule-ID numbers
|
||||
so that you can assign a molecule-ID number to each atom. (I think this
|
||||
is needed to wrap atom coordinates without breaking molecules in half.)
|
||||
|
||||
Of course, you don't have to save your trajectories in DUMP format,
|
||||
(other formats like DCD work fine) I just mention dump files
|
||||
because these are the files I'm familiar with.
|
||||
|
||||
3) ----- Wrap the coordinates to the unit cell
|
||||
(without cutting the molecules in half)
|
||||
|
||||
a) Start VMD
|
||||
b) Load the trajectory in VMD (see above)
|
||||
c) Menu Extensions->Tk Console
|
||||
d) Try entering these commands:
|
||||
|
||||
pbc wrap -compound res -all
|
||||
pbc box
|
||||
|
||||
----- Optional ----
|
||||
Sometimes the solvent or membrane obscures the view of the solute.
|
||||
It can help to shift the location of the periodic boundary box
|
||||
To shift the box in the y direction (for example) do this:
|
||||
|
||||
pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
|
||||
pbc box -shiftcenterrel {0.0 0.15 0.0}
|
||||
|
||||
Distances are measured in units of box-length fractions, not Angstroms.
|
||||
|
||||
Alternately if you have a solute whose atoms are all of type 1,
|
||||
then you can also try this to center the box around it:
|
||||
|
||||
pbc wrap -sel type=1 -all -centersel type=2 -center com
|
||||
|
||||
4)
|
||||
You should check if your periodic boundary conditions are too small.
|
||||
To do that:
|
||||
select Graphics->Representations menu option
|
||||
click on the "Periodic" tab, and
|
||||
click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
|
||||
|
||||
5) Optional: If you like, change the atom types in the PSF file so
|
||||
that VMD recognizes the atom types, use something like:
|
||||
|
||||
sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
|
||||
sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
|
||||
sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
|
||||
|
||||
(If you do this, it might effect step 2 above.)
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 83 KiB |
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Load Diff
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|
After Width: | Height: | Size: 69 KiB |
Binary file not shown.
|
After Width: | Height: | Size: 50 KiB |
Binary file not shown.
|
After Width: | Height: | Size: 66 KiB |
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|
After Width: | Height: | Size: 69 KiB |
|
|
@ -0,0 +1,254 @@
|
|||
# This file defines a 4-helix bundle coarse-grained protein model (AUF2) used in
|
||||
# G. Bellesia, AI Jewett, and J-E Shea,
|
||||
# Protein Science, Vol19 141-154 (2010)
|
||||
#
|
||||
# Strategy:
|
||||
#
|
||||
#1) First I'll define some building blocks (A16, B16, T3)
|
||||
# which are helices, sheets and turns of a predetermined length)
|
||||
#
|
||||
#2) Then I'll copy and paste them together to build
|
||||
# a 4-helix bundle (or a 4-strand beta-barrel).
|
||||
# This approach is optional. If your protein has helices which are not
|
||||
# identical, you should probably just include all 4 helices in a single
|
||||
# "Data Atoms" section and don't try to subdivide the protein into pieces.)
|
||||
|
||||
|
||||
|
||||
1beadProtSci2010 { # <-- enclose definitions in a namespace for portability
|
||||
|
||||
# A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each)
|
||||
|
||||
A16 {
|
||||
|
||||
# AtomID MoleculeID AtomType Charge X Y Z
|
||||
|
||||
write('Data Atoms') {
|
||||
$atom:a1 $mol:... @atom:../sL 0.0 -2.4 -2.4 0.0
|
||||
$atom:a2 $mol:... @atom:../sL 0.0 2.4 -2.4 3.6
|
||||
$atom:a3 $mol:... @atom:../sH 0.0 2.4 2.4 7.2
|
||||
$atom:a4 $mol:... @atom:../sH 0.0 -2.4 2.4 10.8
|
||||
$atom:a5 $mol:... @atom:../sL 0.0 -2.4 -2.4 14.4
|
||||
$atom:a6 $mol:... @atom:../sL 0.0 2.4 -2.4 18.0
|
||||
$atom:a7 $mol:... @atom:../sH 0.0 2.4 2.4 21.6
|
||||
$atom:a8 $mol:... @atom:../sH 0.0 -2.4 2.4 25.2
|
||||
$atom:a9 $mol:... @atom:../sL 0.0 -2.4 -2.4 28.8
|
||||
$atom:a10 $mol:... @atom:../sL 0.0 2.4 -2.4 32.4
|
||||
$atom:a11 $mol:... @atom:../sH 0.0 2.4 2.4 36.0
|
||||
$atom:a12 $mol:... @atom:../sH 0.0 -2.4 2.4 39.6
|
||||
$atom:a13 $mol:... @atom:../sL 0.0 -2.4 -2.4 43.2
|
||||
$atom:a14 $mol:... @atom:../sL 0.0 2.4 -2.4 46.8
|
||||
$atom:a15 $mol:... @atom:../sH 0.0 2.4 2.4 50.4
|
||||
$atom:a16 $mol:... @atom:../sH 0.0 -2.4 2.4 54.0
|
||||
}
|
||||
|
||||
write('Data Bonds') {
|
||||
$bond:b1 @bond:../backbone $atom:a1 $atom:a2
|
||||
$bond:b2 @bond:../backbone $atom:a2 $atom:a3
|
||||
$bond:b3 @bond:../backbone $atom:a3 $atom:a4
|
||||
$bond:b4 @bond:../backbone $atom:a4 $atom:a5
|
||||
$bond:b5 @bond:../backbone $atom:a5 $atom:a6
|
||||
$bond:b6 @bond:../backbone $atom:a6 $atom:a7
|
||||
$bond:b7 @bond:../backbone $atom:a7 $atom:a8
|
||||
$bond:b8 @bond:../backbone $atom:a8 $atom:a9
|
||||
$bond:b9 @bond:../backbone $atom:a9 $atom:a10
|
||||
$bond:b10 @bond:../backbone $atom:a10 $atom:a11
|
||||
$bond:b11 @bond:../backbone $atom:a11 $atom:a12
|
||||
$bond:b12 @bond:../backbone $atom:a12 $atom:a13
|
||||
$bond:b13 @bond:../backbone $atom:a13 $atom:a14
|
||||
$bond:b14 @bond:../backbone $atom:a14 $atom:a15
|
||||
$bond:b15 @bond:../backbone $atom:a15 $atom:a16
|
||||
}
|
||||
|
||||
} # A16
|
||||
|
||||
|
||||
T3 { # T3 is a "turn" region consisting of 3 beads
|
||||
|
||||
# AtomID MoleculeID AtomType Charge X Y Z
|
||||
|
||||
write('Data Atoms') {
|
||||
$atom:a1 $mol:... @atom:../tN 0.0 -4.8 0.0 0.0
|
||||
$atom:a2 $mol:... @atom:../tN 0.0 0.0 3.3 -1.44
|
||||
$atom:a3 $mol:... @atom:../tN 0.0 4.8 0.0 0.0
|
||||
}
|
||||
|
||||
write('Data Bonds') {
|
||||
$bond:b1 @bond:../backbone $atom:a1 $atom:a2
|
||||
$bond:b2 @bond:../backbone $atom:a2 $atom:a3
|
||||
}
|
||||
|
||||
} # T3
|
||||
|
||||
|
||||
# ----- Now build a larger molecule using A16 and T3 -------
|
||||
|
||||
# Create a 4-Helix bundle.
|
||||
# In this version, the hydrophobic beads are poing outward.
|
||||
# I oriented them this way because I want to place this protein in a membrane.
|
||||
# (There is another file in this directory containing alternate version
|
||||
# of this same molecule with the hydrophobic beads pointing inward.)
|
||||
|
||||
4HelixInsideOut {
|
||||
helix1 = new A16.rot(-225, 0,0,1).move(-5.70,-5.70,-32.4)
|
||||
helix2 = new A16.rot(-135, 0,0,1).move( 5.70,-5.70,-28.8)
|
||||
helix3 = new A16.rot( -45, 0,0,1).move( 5.70, 5.70,-25.2)
|
||||
helix4 = new A16.rot( 45, 0,0,1).move(-5.70, 5.70,-21.6)
|
||||
|
||||
turn1 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot( 10,0,0,1).move(0.78,-4.2, 27.9)
|
||||
turn2 = new T3.rot(-10,1,0,0).rot( 20,0,1,0).rot(-70,0,0,1).move(4.55, 2.4,-33.0)
|
||||
turn3 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot(190,0,0,1).move(-0.78,4.2, 34.2)
|
||||
|
||||
write('Data Bonds') {
|
||||
$bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16
|
||||
$bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16
|
||||
$bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1
|
||||
$bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1
|
||||
$bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16
|
||||
$bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16
|
||||
}
|
||||
create_var { $mol } # molecule ID number shared by all atoms in this protein
|
||||
|
||||
} # 4HelixInsideOut
|
||||
|
||||
|
||||
# -------- Minor coordinates adjustment: -----------
|
||||
|
||||
# Those coordinates in the commands above are a little too large.
|
||||
# To make it easier to type them in, I was using sigma=6.0 Angstroms.
|
||||
# Instead, here I'll try using sigma=5.5 Angstroms. 5.5/6 = 0.916667)
|
||||
|
||||
4HelixInsideOut.scale(0.9166666666666666)
|
||||
|
||||
# Note: "scale()" only effects the initial coordinates of
|
||||
# the molecule, not the force field parameters.
|
||||
# (If you plan to minimize the molecule, you don't need to
|
||||
# be so careful about the initial coordinates. In that case,
|
||||
# you don't have worry about "scale()". Feel free to remove.)
|
||||
|
||||
|
||||
|
||||
# -------------- Force-Field Parameters ------------
|
||||
|
||||
# Units and force-field styles for this protein model
|
||||
# (These can be overridden later.)
|
||||
|
||||
write_once("In Init") {
|
||||
units real
|
||||
atom_style full
|
||||
bond_style hybrid harmonic
|
||||
angle_style hybrid harmonic
|
||||
dihedral_style hybrid fourier
|
||||
pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 21.0 24.0
|
||||
pair_modify mix arithmetic
|
||||
special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions)
|
||||
}
|
||||
|
||||
# --- Distance Units ---
|
||||
# In this version of the model, sigma (the bond-length
|
||||
# and particle diameter) is rounded to 5.5 Angstroms.
|
||||
#
|
||||
# --- Energy & Temperature Units ---
|
||||
# In this protein model, "epsilon" represents the free energy
|
||||
# bonus for bringing two hydrophobic amino acids together.
|
||||
# Here I choose to set epsilon to 1.806551818181818 kCal/mole.
|
||||
# This value was chosen so that a temperature of 300 Kelvin lies at
|
||||
# 0.33 epsilon, which is the unfolding temperature of the marginally stable
|
||||
# "ASF1" protein model from the Bellesia et al 2010 paper.
|
||||
# This choice insures that both the "ASF1" model from that paper,
|
||||
# as well as the much more stable "AUF2" protein we use here (which
|
||||
# unfolds at 0.42*eps) should definitely remain stable at 300 degrees Kelvin,
|
||||
# in the bulk at least. (However it's not clear that these energy
|
||||
# parameters will work well for a protein in membrane. Perhaps I'll
|
||||
# run some tests and fine tune these parameters for this scenario.)
|
||||
|
||||
|
||||
# 2-body (non-bonded) interactions:
|
||||
#
|
||||
# Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6)
|
||||
#
|
||||
# i j pairstylename eps sig K L
|
||||
#
|
||||
write_once("In Settings") {
|
||||
pair_coeff @atom:sH @atom:sH lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1
|
||||
pair_coeff @atom:sL @atom:sL lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0
|
||||
pair_coeff @atom:tN @atom:tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0
|
||||
}
|
||||
|
||||
# The exact value of the bond_coeff does not matter too much as long as
|
||||
# it is "stiff enough". Here I use a softer bond spring than the one
|
||||
# used in the paper so that I can increase the time step.
|
||||
# I also use a relatively soft spring to constrain the bond angles.
|
||||
|
||||
# bond_coeff bondType bondstylename k r0
|
||||
|
||||
write_once("In Settings") {
|
||||
bond_coeff @bond:1beadProtSci2010/backbone harmonic 10.0 5.5
|
||||
}
|
||||
|
||||
|
||||
|
||||
# We use the same bond-angle forces whenever
|
||||
# there are 3 consecutively-bonded atoms:
|
||||
#
|
||||
# angleType atomtypes1 2 3 bondtypes1 2
|
||||
|
||||
write_once("Data Angles By Type") {
|
||||
@angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:*
|
||||
}
|
||||
|
||||
# angle_coeff angleType anglestylename k theta0
|
||||
write_once("In Settings") {
|
||||
angle_coeff @angle:backbone harmonic 100.0 105.0
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
# Dihedral interactions are also determined by atom-type name in this case.
|
||||
# I chose atoms whose type-names begin with "t" to be "turn" atoms.
|
||||
# Atoms whose type-names begin with "s" could be either helices or sheets.
|
||||
# (In this case, helices. In this example, we use the @dihedral:delta65_0
|
||||
# parameters. This corresponds to the "AUF2" model from the
|
||||
# Bellesia et. al 2010 paper.)
|
||||
|
||||
# dihedralType atomtypes1 2 3 4 bondtypes1 2 3
|
||||
|
||||
write_once("Data Dihedrals By Type") {
|
||||
@dihedral:delta65_0 @atom:s* @atom:s* @atom:s* @atom:s* * * *
|
||||
|
||||
# If "tN" (turn) atoms are present, use the @dihedral:turn parameters
|
||||
|
||||
@dihedral:turn @atom:tN @atom:* @atom:* @atom:* * * *
|
||||
}
|
||||
|
||||
|
||||
# From the Bellesia et al 2010 paper:
|
||||
# for helices: U_{dih}(\phi) = 1.2*(cos(3\phi) + cos(\phi+\delta))
|
||||
# for turns: U_{dih}(\phi) = 0.2*cos(3\phi)
|
||||
#
|
||||
# General formula used for "dihedral_style fourier":
|
||||
# U_{dih}(\phi) = \Sum_{i=1}^m K_i [ 1.0 + cos(n_i \phi - d_i) ]
|
||||
#
|
||||
# Syntax:
|
||||
# dihedralType dihedralstyle m K_1 n_1 d_1 K2 n_2 d_2 ...
|
||||
|
||||
write_once("In Settings") {
|
||||
dihedral_coeff @dihedral:delta60_0 fourier 2 2.167862 3 0 2.167862 1 -60.0
|
||||
dihedral_coeff @dihedral:delta62_5 fourier 2 2.167862 3 0 2.167862 1 -62.5
|
||||
dihedral_coeff @dihedral:delta65_0 fourier 2 2.167862 3 0 2.167862 1 -65.0
|
||||
dihedral_coeff @dihedral:turn fourier 1 0.361310 3 0
|
||||
# Note: 2.167862=1.2*epsilon and 0.361310=0.2*epsilon.
|
||||
}
|
||||
|
||||
|
||||
# --- Mass Units ---
|
||||
# Typical amino acids weigh approximately 110.0 grams/mole. (Rounding down):
|
||||
write_once("Data Masses") {
|
||||
@atom:1beadProtSci2010/sH 100.0
|
||||
@atom:1beadProtSci2010/sL 100.0
|
||||
@atom:1beadProtSci2010/tN 100.0
|
||||
}
|
||||
|
||||
} # 1beadProtSci2010 (namespace)
|
||||
|
||||
|
|
@ -0,0 +1,225 @@
|
|||
### THIS FILE IS OPTIONAL AND IS NOT NECESSARY. IN THIS FILE, I DEFINED SOME ##
|
||||
### ADDITIONAL PROTEIN TYPES FROM THE PAPER THAT I DID NOT USE IN THIS EXAMPLE##
|
||||
#
|
||||
# This file defines a family of coarse-grained protein models used in:
|
||||
# G. Bellesia, AI Jewett, and J-E Shea,
|
||||
# Protein Science, Vol19 141-154 (2010)
|
||||
#
|
||||
# Strategy:
|
||||
#
|
||||
#1) First I'll define some building blocks (A16, B16, T3)
|
||||
# which are helices, sheets and turns of a predetermined length)
|
||||
|
||||
import "1beadProtSci2010.lt"
|
||||
|
||||
# We defined A16 and T3 earlier in "1beadPRotSci2010.lt" Will define B16 below
|
||||
#
|
||||
#2) Then I'll copy and paste them together to build
|
||||
# a 4-helix bundle or a 4-strand beta-barrel.
|
||||
|
||||
|
||||
1beadProtSci2010 { #<-- Add new molecules to existing namespace defined earlier
|
||||
# This way we don't have to start from scratch. We can
|
||||
# use all the atom types and angle settings defined earlier
|
||||
|
||||
# B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each)
|
||||
|
||||
B16 {
|
||||
|
||||
# AtomID MoleculeID AtomType Charge X Y Z
|
||||
|
||||
write('Data Atoms') {
|
||||
$atom:a1 $mol:... @atom:../sL 0.0 -1.8 0.0 0.0
|
||||
$atom:a2 $mol:... @atom:../sH 0.0 1.8 0.0 4.8
|
||||
$atom:a3 $mol:... @atom:../sL 0.0 -1.8 0.0 9.6
|
||||
$atom:a4 $mol:... @atom:../sH 0.0 1.8 0.0 14.4
|
||||
$atom:a5 $mol:... @atom:../sL 0.0 -1.8 0.0 19.2
|
||||
$atom:a6 $mol:... @atom:../sH 0.0 1.8 0.0 24.0
|
||||
$atom:a7 $mol:... @atom:../sL 0.0 -1.8 0.0 28.8
|
||||
$atom:a8 $mol:... @atom:../sH 0.0 1.8 0.0 33.6
|
||||
$atom:a9 $mol:... @atom:../sL 0.0 -1.8 0.0 38.4
|
||||
$atom:a10 $mol:... @atom:../sH 0.0 1.8 0.0 43.2
|
||||
$atom:a11 $mol:... @atom:../sL 0.0 -1.8 0.0 48.0
|
||||
$atom:a12 $mol:... @atom:../sH 0.0 1.8 0.0 52.8
|
||||
$atom:a13 $mol:... @atom:../sL 0.0 -1.8 0.0 57.6
|
||||
$atom:a14 $mol:... @atom:../sH 0.0 1.8 0.0 62.4
|
||||
$atom:a15 $mol:... @atom:../sL 0.0 -1.8 0.0 67.2
|
||||
$atom:a16 $mol:... @atom:../sH 0.0 1.8 0.0 72.0
|
||||
}
|
||||
|
||||
write('Data Bonds') {
|
||||
$bond:b1 @bond:../backbone $atom:a1 $atom:a2
|
||||
$bond:b2 @bond:../backbone $atom:a2 $atom:a3
|
||||
$bond:b3 @bond:../backbone $atom:a3 $atom:a4
|
||||
$bond:b4 @bond:../backbone $atom:a4 $atom:a5
|
||||
$bond:b5 @bond:../backbone $atom:a5 $atom:a6
|
||||
$bond:b6 @bond:../backbone $atom:a6 $atom:a7
|
||||
$bond:b7 @bond:../backbone $atom:a7 $atom:a8
|
||||
$bond:b8 @bond:../backbone $atom:a8 $atom:a9
|
||||
$bond:b9 @bond:../backbone $atom:a9 $atom:a10
|
||||
$bond:b10 @bond:../backbone $atom:a10 $atom:a11
|
||||
$bond:b11 @bond:../backbone $atom:a11 $atom:a12
|
||||
$bond:b12 @bond:../backbone $atom:a12 $atom:a13
|
||||
$bond:b13 @bond:../backbone $atom:a13 $atom:a14
|
||||
$bond:b14 @bond:../backbone $atom:a14 $atom:a15
|
||||
$bond:b15 @bond:../backbone $atom:a15 $atom:a16
|
||||
}
|
||||
|
||||
} # B16
|
||||
|
||||
# ----- Now build larger molecules using B16 and T3 -------
|
||||
|
||||
|
||||
4SheetBarrel {
|
||||
sheet1 = new B16.rot( 45, 0,0,1).move(-4.762203156,-4.762203156, -36.0)
|
||||
sheet2 = new B16.rot( 135, 0,0,1).move( 4.762203156,-4.762203156, -36.0)
|
||||
sheet3 = new B16.rot( 225, 0,0,1).move( 4.762203156, 4.762203156, -36.0)
|
||||
sheet4 = new B16.rot( 315, 0,0,1).move(-4.762203156, 4.762203156, -36.0)
|
||||
|
||||
turn1 = new T3.rot(180,1,0,0).rot( 0, 0,0,1).move( 0, -7.8, 39.6)
|
||||
turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(4.2, 0.0,-41.4)
|
||||
turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move( 0, 7.8, 39.6)
|
||||
|
||||
write('Data Bonds') {
|
||||
$bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16
|
||||
$bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16
|
||||
$bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1
|
||||
$bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1
|
||||
$bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16
|
||||
$bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16
|
||||
}
|
||||
create_var { $mol } # molecule ID number shared by all atoms in this protein
|
||||
}
|
||||
|
||||
|
||||
# Below I define several alternate conformations of the"4HelixBundleInsideOut"
|
||||
# molecule I defined earlier in "1beadProtSci2010.lt". Same molecule however.
|
||||
|
||||
4HelixBundle {
|
||||
helix1 = new A16.rot( -45, 0,0,1).move(-5.70,-5.70,-32.4)
|
||||
helix2 = new A16.rot( 45, 0,0,1).move( 5.70,-5.70,-28.8)
|
||||
helix3 = new A16.rot( 135, 0,0,1).move( 5.70, 5.70,-25.2)
|
||||
helix4 = new A16.rot( 225, 0,0,1).move(-5.70, 5.70,-21.6)
|
||||
|
||||
write('Data Bonds') {
|
||||
$bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16
|
||||
$bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16
|
||||
$bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1
|
||||
$bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1
|
||||
$bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16
|
||||
$bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16
|
||||
}
|
||||
|
||||
turn1 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot( 8,0,0,1).move(-3.6,-4.8,28.2)
|
||||
turn2 = new T3.rot(-5,1,0,0).rot( 21,0,1,0).rot(-100,0,0,1).move(4.2,-0.66,-30.9)
|
||||
turn3 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot(188,0,0,1).move(3.6,4.8,35.4)
|
||||
|
||||
create_var { $mol } # molecule ID number shared by all atoms in this protein
|
||||
|
||||
} # 4HelixBundle
|
||||
|
||||
|
||||
|
||||
|
||||
# --- alternate conformations (same molecule) ----
|
||||
|
||||
# In the following version, the helices are oriented in a similar way,
|
||||
# but they are separated a little further away from eachother.
|
||||
|
||||
4HelixBundleLoose {
|
||||
|
||||
helix1 = new A16.rot( -45, 0,0,1).move(-6.7347723,-6.7347723, -27.0)
|
||||
helix2 = new A16.rot( 45, 0,0,1).move( 6.7347723,-6.7347723, -27.0)
|
||||
helix3 = new A16.rot( 135, 0,0,1).move( 6.7347723, 6.7347723, -27.0)
|
||||
helix4 = new A16.rot( 225, 0,0,1).move(-6.7347723, 6.7347723, -27.0)
|
||||
|
||||
turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-1.2,-4.2,32.4)
|
||||
turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(4.2,-0.9,-28.8)
|
||||
turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(1.2,4.2,32.4)
|
||||
|
||||
write('Data Bonds') {
|
||||
$bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16
|
||||
$bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16
|
||||
$bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1
|
||||
$bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1
|
||||
$bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16
|
||||
$bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16
|
||||
}
|
||||
create_var { $mol } # molecule ID number shared by all atoms in this protein
|
||||
}
|
||||
|
||||
|
||||
# In following version, the helices are oriented in a similar way,
|
||||
# but they are separated a little further away from eachother.
|
||||
|
||||
4HelixInsideOutLoose {
|
||||
helix1 = new A16.rot(-225, 0,0,1).move(-6.7347723,-6.7347723, -27.0)
|
||||
helix2 = new A16.rot(-135, 0,0,1).move( 6.7347723,-6.7347723, -27.0)
|
||||
helix3 = new A16.rot( -45, 0,0,1).move( 6.7347723, 6.7347723, -27.0)
|
||||
helix4 = new A16.rot( 45, 0,0,1).move(-6.7347723, 6.7347723, -27.0)
|
||||
|
||||
turn1 = new T3.rot(180,1,0,0).rot( 10,0,0,1).move( 0.78,-4.2,28.8)
|
||||
turn2 = new T3.rot( 70,1,0,0).rot(-70,0,0,1).move( 10.8,2.4,-28.2)
|
||||
turn3 = new T3.rot(180,1,0,0).rot(190,0,0,1).move(-0.78,4.2,28.8)
|
||||
|
||||
write('Data Bonds') {
|
||||
$bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16
|
||||
$bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16
|
||||
$bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1
|
||||
$bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1
|
||||
$bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16
|
||||
$bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16
|
||||
}
|
||||
create_var { $mol } # molecule ID number shared by all atoms in this protein
|
||||
|
||||
} # 4HelixInsideOutLoose
|
||||
|
||||
|
||||
|
||||
|
||||
# In the following version, the 4 helices are arranged next to each other,
|
||||
# side-by-side, in a planar conformation (instead of a compact bundle).
|
||||
|
||||
4HelixPlanar {
|
||||
helix1 = new A16.rot(-00, 0,0,1).move(0, 0, -27.0)
|
||||
helix2 = new A16.rot( 00, 0,0,1).move(14.4, 0, -27.0)
|
||||
helix3 = new A16.rot(-00, 0,0,1).move(28.8, 0, -27.0)
|
||||
helix4 = new A16.rot( 00, 0,0,1).move(43.2, 0, -27.0)
|
||||
|
||||
turn1 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move( 4.8, 0, 31.8)
|
||||
turn2 = new T3.rot( 0,1,0,0).rot(180,0,0,1).move(19.2, 0,-31.8)
|
||||
turn3 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move(34.6, 0, 31.8)
|
||||
|
||||
write('Data Bonds') {
|
||||
$bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16
|
||||
$bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16
|
||||
$bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1
|
||||
$bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1
|
||||
$bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16
|
||||
$bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16
|
||||
}
|
||||
create_var { $mol } # molecule ID number shared by all atoms in this protein
|
||||
|
||||
} # 4HelixPlanar
|
||||
|
||||
|
||||
# -------- Minor coordinates adjustment: -----------
|
||||
# Those coordinates in the commands above are a little too large.
|
||||
# To make it easier to type them in, I was using sigma=6.0 Angstroms.
|
||||
# Instead, here I'll try using sigma=5.5 Angstroms. 5.5/6 = 0.916667)
|
||||
|
||||
4SheetBarrel.scale(0.9166666666666666)
|
||||
4HelixBundle.scale(0.9166666666666666)
|
||||
4HelixBundleLoose.scale(0.9166666666666666)
|
||||
4HelixInsideOutLoose.scale(0.9166666666666666)
|
||||
4HelixPlanar.scale(0.9166666666666666)
|
||||
|
||||
# Note: "scale()" only effects the initial coordinates of
|
||||
# the molecule, not the force field parameters.
|
||||
# (If you plan to minimize the molecule, you don't need to
|
||||
# be so careful about the initial coordinates. In that case,
|
||||
# you don't have worry about "scale()". Feel free to remove.)
|
||||
|
||||
|
||||
} # 1beadProtSci2010 (namespace)
|
||||
|
||||
|
|
@ -0,0 +1,198 @@
|
|||
# Note:
|
||||
#
|
||||
# This example may require additional features to be added to LAMMPS. If
|
||||
# LAMMPS complains about an "Invalid pair_style", then download copy the
|
||||
# "additional_lammps_code" from moltemplate.org, unpack it into your LAMMPS
|
||||
# "src" directory and recompile LAMMPS.
|
||||
#
|
||||
# -------- Description --------
|
||||
#
|
||||
# This example contains an implementation of the DPPC lipid bilayer described in
|
||||
# G. Brannigan, P.F. Philips, and F.L.H. Brown,
|
||||
# Physical Review E, Vol 72, 011915 (2005)
|
||||
# and:
|
||||
# M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown
|
||||
# J. Chem. Phys. 135, 244701 (2011)
|
||||
#
|
||||
# As in Watson(JCP 2011), rigid bond-length constraints have been replaced
|
||||
# by harmonic bonds.
|
||||
#
|
||||
# A truncated version of this lipid (named "DLPC") has also been added.
|
||||
# Unlike the original "DPPC" molecule model, "DLPC" has not been carefully
|
||||
# parameterized to reproduce the correct behavior in a lipid bilayer mixture.
|
||||
#
|
||||
# Units:
|
||||
#
|
||||
# The "epsilon" parameter in their model is approximately 2.75 kJ/mole
|
||||
# ( = 0.657265774378585 kCal/mole, using 1kCal=4.184kJ)
|
||||
# The "sigma" parameter corresponds to 7.5 angstroms.
|
||||
|
||||
|
||||
CGLipidBr2005 {
|
||||
|
||||
|
||||
write_once("In Init") {
|
||||
# -- Default styles for "CGLipidBr2005" --
|
||||
units real
|
||||
atom_style full
|
||||
# (Hybrid force field styles were used for portability.)
|
||||
bond_style hybrid harmonic
|
||||
|
||||
#angle_style hybrid cosine/delta # <- used in the original article
|
||||
angle_style hybrid harmonic # <- prevents unphysical acute angle turns
|
||||
# Explanation:
|
||||
# angle_style cosine/delta: U(theta) = k*(1-cos(theta-theta0))
|
||||
# angle_style harmonic: U(theta) = k*(theta-theta0)^2
|
||||
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
pair_style hybrid table linear 1130 &
|
||||
lj/charmm/coul/charmm/inter es4k4l 14.5 15
|
||||
pair_modify mix arithmetic
|
||||
special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds"
|
||||
|
||||
neighbor 2.0 multi # <- perhaps unnecessary
|
||||
communicate multi # <- perhaps unnecessary
|
||||
}
|
||||
|
||||
|
||||
DPPC {
|
||||
write("Data Atoms") {
|
||||
$atom:h $mol:. @atom:head 0.0 0.00 0.00 33.75 # DPPC head atom
|
||||
$atom:i $mol:. @atom:../int 0.0 -1.00 0.00 26.25
|
||||
$atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 18.75
|
||||
$atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 11.25
|
||||
$atom:t3 $mol:. @atom:../tail 0.0 1.00 0.00 3.75
|
||||
}
|
||||
write("Data Bonds") {
|
||||
$bond:b1 @bond:../backbone $atom:h $atom:i
|
||||
$bond:b2 @bond:../backbone $atom:i $atom:t1
|
||||
$bond:b3 @bond:../backbone $atom:t1 $atom:t2
|
||||
$bond:b4 @bond:../backbone $atom:t2 $atom:t3
|
||||
}
|
||||
write("Data Angles") {
|
||||
$angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1
|
||||
$angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2
|
||||
$angle:a3 @angle:../backbone $atom:t1 $atom:t2 $atom:t3
|
||||
}
|
||||
|
||||
# Define properties of the local (lipid-specific) atom:head type atom:
|
||||
write_once("Data Masses") {
|
||||
@atom:head 200.0
|
||||
}
|
||||
write_once("In Settings") {
|
||||
pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
}
|
||||
|
||||
} #DPPC
|
||||
|
||||
|
||||
DLPC {
|
||||
write("Data Atoms") {
|
||||
$atom:h $mol:. @atom:head 0.0 0.00 0.00 30.00 # DLPC head atom
|
||||
$atom:i $mol:. @atom:../int 0.0 -1.00 0.00 22.50
|
||||
$atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 15.00
|
||||
$atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 7.50
|
||||
}
|
||||
write("Data Bonds") {
|
||||
$bond:b1 @bond:../backbone $atom:h $atom:i
|
||||
$bond:b2 @bond:../backbone $atom:i $atom:t1
|
||||
$bond:b3 @bond:../backbone $atom:t1 $atom:t2
|
||||
}
|
||||
write("Data Angles") {
|
||||
$angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1
|
||||
$angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2
|
||||
}
|
||||
# Define properties of the local (lipid-specific) atom:head type atom:
|
||||
write_once("Data Masses") {
|
||||
@atom:head 200.0
|
||||
}
|
||||
write_once("In Settings") {
|
||||
pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
}
|
||||
} #DLPC
|
||||
|
||||
|
||||
# Particles and properties shared by all lipid types:
|
||||
|
||||
write_once("Data Masses") {
|
||||
@atom:int 200.0
|
||||
@atom:tail 200.0
|
||||
@atom:head 200.0 #<- Default head type. We may override it later.
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
# -- Default settings/parameters for "CGLipidBr2005" --
|
||||
# (Hybrid bond & angle styles were used for portability.)
|
||||
|
||||
# As in Watson(JCP 2011), rigid bond-length constraints
|
||||
# have been replaced by harmonic bonds.
|
||||
# The k_theta parameter should lie in between 5*epsilon and 10*epsilon.
|
||||
bond_coeff @bond:backbone harmonic 116.847 7.5 #<--2*5000*eps/sig^2
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
# cosine/delta: U(theta) = k*(1-cos(theta-theta0))
|
||||
#angle_coeff @angle:backbone cosine/delta 4.60086042 180 #<-- 7*eps
|
||||
# harmonic: U(theta) = k*(theta-theta0)^2 not (k/2)*(theta-theta0)^2
|
||||
angle_coeff @angle:backbone harmonic 9.85898661 180 #<-->30*eps
|
||||
}
|
||||
# I use a stiffer bond-angle than the original Brannigan & Brown 2005 paper
|
||||
# to attempt to compensate for the fact that here we are using a lipid
|
||||
# mixture of DPPC and DLPC. (The mixture of lipids introduces a great deal
|
||||
# of disorder into the bilayer which would not be present in a DPPC bilayer.
|
||||
# This causes pores to form. Increasing the angle stiffness prevents this.)
|
||||
|
||||
write_once("In Settings") {
|
||||
|
||||
# The interaction of "atom:int" with other "atom:int" atoms is given by
|
||||
# epsilon*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2), shifted and cutoff at
|
||||
# r=3*sigma. This was implemented using pair_style table.
|
||||
# Unfortunately, mixing lj/charmm and "table" pair styles in the same
|
||||
# simulation is very inneficient.
|
||||
|
||||
pair_coeff @atom:int @atom:int table table_int.dat INT
|
||||
|
||||
# The interaction of tail beads with eachother is given by the formula below
|
||||
# and with other atoms ...using Lorenz-Berthelot and "repulsive wins" rules:
|
||||
# epsilon*(0.4*(sigma/r)^12 - 1.0*(sigma/r)^6),
|
||||
pair_coeff @atom:tail @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1
|
||||
pair_coeff @atom:int @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1
|
||||
|
||||
# The interaction of head beads which all other beads is given by:
|
||||
# epsilon*(0.4*(sigma/r)^12 - 0.0*(sigma/r)^6),
|
||||
|
||||
pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
pair_coeff @atom:int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
|
||||
|
||||
} # write_once("In Settings")
|
||||
|
||||
# Note: I divided epsilon by 4 to get "0.1643" because we are using the
|
||||
# "es4k4l" coeffstyle, corresponding to U(r)=eps(4*K*(s/r)^12 + 4*L*(s/r)^6)
|
||||
# (The "es4k4l" coeffstyle is the default.) Using this convention makes it
|
||||
# easier to mix this coarse-grained lipid model with other molecular models.
|
||||
|
||||
|
||||
|
||||
} # CGLipidBr2005
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
# Note: This example has not been optimized for speed.
|
||||
#
|
||||
# Unfortunately, using both lj/charmm and "table" pair styles in the same
|
||||
# simulation seems to be very inneficient. (The simulation is twice as slow
|
||||
# as using only the "lj/charmm" pair styles for every pairwise interaction,
|
||||
# ...and about 25% slower than using "table" for every pairwise interaction.
|
||||
# However the lennard-jones pair styles support mixing, so we use them to
|
||||
# make it easier to run these molecules with other molecules which don't use
|
||||
# pair_table. I felt that portability was worth the extra 25% slow down.)
|
||||
|
||||
|
|
@ -0,0 +1,34 @@
|
|||
#!/usr/bin/env python
|
||||
|
||||
# Calculate a table of pairwise energies and forces between "INT" atoms
|
||||
# in the lipid membrane model described in
|
||||
# Brannigan et al, Phys Rev E, 72, 011915 (2005)
|
||||
# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2)
|
||||
# However it is truncated at rc2 = 22.5 (shifted upwards to maintain continuity)
|
||||
|
||||
# The previous version included the repulsive core term
|
||||
def U(r, eps, sigma):
|
||||
return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r))
|
||||
def F(r, eps, sigma):
|
||||
return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r))
|
||||
# We don't want to do that. Instead compute the core repulsion using a
|
||||
# different pair_style and add the attractive term on top of it using the table.
|
||||
# This way it the core repulsion acts as a default interaction with other atom
|
||||
# types (using the new repulsive mixing rules).
|
||||
|
||||
epsilon = 2.75/4.184 # kCal/mole
|
||||
sigma = 7.5
|
||||
Rmin = 0.02
|
||||
Rmax = 22.6
|
||||
rcut = 22.5
|
||||
N = 1130
|
||||
|
||||
for i in range(0,N):
|
||||
r = Rmin + i*(Rmax-Rmin)/(N-1)
|
||||
U_r = U(r, epsilon, sigma) - U(rcut, epsilon, sigma)
|
||||
F_r = F(r, epsilon, sigma)
|
||||
if r > rcut:
|
||||
U_r = 0.0
|
||||
F_r = 0.0
|
||||
print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))
|
||||
|
||||
|
|
@ -0,0 +1,70 @@
|
|||
#!/usr/bin/env python
|
||||
|
||||
# Calculate a table of pairwise energies and forces between "INT" atoms
|
||||
# in the lipid membrane model described in
|
||||
# Brannigan et al, Phys Rev E, 72, 011915 (2005)
|
||||
# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2)
|
||||
# I realized later this is not what we want because although energy is conserved
|
||||
# all enrgies are shifted with respect to energies used in the Brannigan paper
|
||||
# (by 0.27 kCal/mole) and the later Watson JCP 2011 paper (by 0.224 kCal/mole).
|
||||
# (So don't use this.)
|
||||
|
||||
# Calculate and print a
|
||||
|
||||
def S(r, rc1, rc2, derivative=False):
|
||||
"""
|
||||
Calculate the switching function S(r) which decays continuously
|
||||
between 1 and 0 in the range from rc1 to rc2 (rc2>rc1):
|
||||
S(r) = (rc2^2 - r^2)^2 * (rc2^2 + 2*r^2 - 3*rc1^2) / (rc2^2-rc1^2)^3
|
||||
I'm using the same smoothing/switching cutoff function used by the CHARMM
|
||||
force-fields. (I'm even using the same code to implement it, taken
|
||||
from lammps charmm/coul/charmm pair style, rewritten in python.)
|
||||
|
||||
"""
|
||||
assert(rc2>rc1)
|
||||
rsq = r*r
|
||||
rc1sq = rc1*rc1
|
||||
rc2sq = rc2*rc2
|
||||
denom_lj_inv = (1.0 / ((rc2sq-rc1sq)*
|
||||
(rc2sq-rc1sq)*
|
||||
(rc2sq-rc1sq)))
|
||||
if rsq > rc2sq:
|
||||
return 0.0
|
||||
elif rsq < rc1sq:
|
||||
if derivative:
|
||||
return 0.0
|
||||
else:
|
||||
return 1.0
|
||||
else:
|
||||
rc2sq_minus_rsq = (rc2sq - rsq)
|
||||
rc2sq_minus_rsq_sq = rc2sq_minus_rsq * rc2sq_minus_rsq
|
||||
if derivative:
|
||||
return (12.0 * rsq * rc2sq_minus_rsq * (rsq-rc1sq) * denom_lj_inv)
|
||||
else:
|
||||
return (rc2sq_minus_rsq_sq *
|
||||
(rc2sq + 2.0*rsq - 3.0*rc1sq) * denom_lj_inv)
|
||||
|
||||
|
||||
def U(r, eps, sigma):
|
||||
return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r))
|
||||
|
||||
def F(r, eps, sigma):
|
||||
return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r))
|
||||
|
||||
epsilon = 2.75/4.184 # kCal/mole
|
||||
sigma = 7.5
|
||||
Rmin = 0.02
|
||||
Rmax = 22.6
|
||||
Rc1 = 22.0
|
||||
Rc2 = 22.5
|
||||
N = 1130
|
||||
|
||||
for i in range(0,N):
|
||||
r = Rmin + i*(Rmax-Rmin)/(N-1)
|
||||
U_r = U(r, epsilon, sigma)
|
||||
F_r = F(r, epsilon, sigma)
|
||||
# Multiply U(r) & F(r) by the smoothing/switch function
|
||||
U_r = U_r * S(r, Rc1, Rc2)
|
||||
F_r = U_r * S(r, Rc1, Rc2, True) + F_r * S(r, Rc1, Rc2, False)
|
||||
print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))
|
||||
|
||||
|
|
@ -0,0 +1,207 @@
|
|||
# Description:
|
||||
|
||||
# This example shows how to put a protein (inclusion) in a
|
||||
# lipid bilayer mixture composed of two different lipids (DPPC and DLPC).
|
||||
# The DPPC lipid model is described here:
|
||||
# G. Brannigan, P.F. Philips, and F.L.H. Brown,
|
||||
# Physical Review E, Vol 72, 011915 (2005)
|
||||
# The protein model is described here:
|
||||
# G. Bellesia, AI Jewett, and J-E Shea,
|
||||
# Protein Science, Vol19 141-154 (2010)
|
||||
# The new DLPC model is a truncated version of DPPC,
|
||||
# (Its behaviour has not been rigorously tested.)
|
||||
# Note that 50%/50% mixtures of DPPC & DLPC are commonly used to
|
||||
# build liposomes http://www.ncbi.nlm.nih.gov/pubmed/10620293
|
||||
|
||||
# Note:
|
||||
# This example may require additional features to be added to LAMMPS.
|
||||
# If LAMMPS complains about an "Invalid pair_style", then copy the code
|
||||
# in the "additional_lammps_code" directory into your LAMMPS "src" directory
|
||||
# and recompile LAMMPS.
|
||||
|
||||
|
||||
|
||||
import "CGLipidBr2005.lt"
|
||||
|
||||
using namespace CGLipidBr2005
|
||||
|
||||
# The "= new random" syntax chooses one of several molecules at random
|
||||
|
||||
lipids = new random([DPPC, DLPC], [0.5,0.5], 1234) #"1234"=random_seed
|
||||
[13].move(7.5, 0, 0)
|
||||
[15].move(3.75, 6.49519, 0) # <-- hexagonal lattice
|
||||
[2].rot(180, 1, 0, 0) # <-- 2 monolayers
|
||||
|
||||
# Move all the lipds up to the center of the box
|
||||
|
||||
lipids[*][*][*].move(0,0,75.0)
|
||||
|
||||
|
||||
|
||||
|
||||
# Although this patch of lipids is not square or rectangular, (it looks
|
||||
# like a parallelogram), this is no longer the case after rectangular
|
||||
# periodic boundary conditions are applied. (Check by visualising in VMD.)
|
||||
|
||||
|
||||
write_once("Data Boundary") {
|
||||
0 97.5 xlo xhi
|
||||
0 97.42785792 ylo yhi
|
||||
0 150.0 zlo zhi
|
||||
}
|
||||
|
||||
|
||||
# A note on geometry:
|
||||
# We want to create a bilayer arranged in a hexagonal lattice consisting of
|
||||
# 15 rows (each row is aligned with the x-axis)
|
||||
# 13 columns (aligned at a 60 degree angle from the x axis)
|
||||
# The lattice spacing is 7.5 Angstroms.
|
||||
# When wrapped onto a rectangular box, the dimensions of the system are:
|
||||
# 13 * 7.5 Angstroms in the X direction
|
||||
# 15 * 7.5*sqrt(3)/2 Angstroms in the Y direction
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
# ------------------- protein inclusion ---------------------
|
||||
|
||||
import "1beadProtSci2010.lt"
|
||||
|
||||
using namespace 1beadProtSci2010
|
||||
|
||||
protein = new 4HelixInsideOut
|
||||
|
||||
protein.move(45.0, 25.98076211, 75.0)
|
||||
|
||||
|
||||
# Delete a hole in the membrane to create space for the protein.
|
||||
|
||||
delete lipids[4][2][*]
|
||||
delete lipids[6][2][*]
|
||||
delete lipids[3-6][3][*]
|
||||
delete lipids[3-5][4][*]
|
||||
delete lipids[2-5][5][*]
|
||||
delete lipids[2][6][*]
|
||||
delete lipids[4][6][*]
|
||||
|
||||
# Note: All atom types must include the full path (the name of
|
||||
# the namespace which defined them as well as the atom type name).
|
||||
# (This is because we are no longer inside that namespace.)
|
||||
|
||||
|
||||
write_once("In Settings") {
|
||||
|
||||
# -----------------------------------------------------------
|
||||
# -------- interactions between protein and lipids ----------
|
||||
# -----------------------------------------------------------
|
||||
|
||||
# Interactions between the protein and lipid atoms are usually
|
||||
# determined by mixing rules. (However this is not possible some
|
||||
# for atoms, such as the "int" atoms in the lipid model which
|
||||
# interact using -1/r^2 attraction.) Mixing rules do not make
|
||||
# sense for these atoms so we must explicitly define their
|
||||
# interaction with all other atoms.
|
||||
|
||||
# We want the hydrophobic interactions between hydrophobic residues in
|
||||
# the protein and beads the interior of the lipid to be energetically
|
||||
# similar to the attractive interactions between the lipid tails.
|
||||
#
|
||||
# Note: I made the width of the outward-facing protein beads slightly larger
|
||||
# ("12.5") whenever they interact with the "tail" beads in each lipid
|
||||
# (in order to make the protein wider there).
|
||||
# This hopefully relieves some of the internal negative pressure in the center
|
||||
# of the bilayer which can otherwise rip apart the protein or suck it into
|
||||
# the bilaer. (This is a hack, and I'm not sure if it is necessary.
|
||||
# For different protein or lipid models, you probably don't need this.)
|
||||
#
|
||||
# i j pairstylename eps sig K L
|
||||
|
||||
pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 12.5 0.4 -1
|
||||
pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1
|
||||
|
||||
# To help keep the protein from tilting 90 degrees and burying itself
|
||||
# within the lipid bilayer, we make the turn regions at either
|
||||
# end of the protein (strongly) attracted to the head groups
|
||||
# of the lipid. (In reality, they would probably be attracted
|
||||
# to the water as well.)
|
||||
|
||||
pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1
|
||||
pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1
|
||||
|
||||
# All other interactions between proteins and lipids are steric.
|
||||
|
||||
pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
|
||||
pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
|
||||
pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
|
||||
pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
|
||||
|
||||
# -----------------------------------------------------------
|
||||
# -------- Modifications to the protein model: --------------
|
||||
# -----------------------------------------------------------
|
||||
#
|
||||
# Turn off attraction between the hydrophobic "@atom:sH" beads:
|
||||
# (These beads are located in the outside of a trans-membrane protein.)
|
||||
|
||||
pair_coeff @atom:1beadProtSci2010/sH @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0
|
||||
|
||||
# (Why: These beads are only attracted to
|
||||
# each other in an aqueous environment)
|
||||
|
||||
# ... and
|
||||
# Turn ON attraction between the hydrophilic "@atom:sL" beads.
|
||||
# (These beads are located in the interior of a trans-membrane protein.)
|
||||
|
||||
pair_coeff @atom:1beadProtSci2010/sL @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1
|
||||
|
||||
# Why?
|
||||
# In reality, polar groups in the interior of trans-membrane
|
||||
# proteins do form hydrogen bonds with each other. This was
|
||||
# absent from the original protein model because, in an aqueous
|
||||
# environment, these groups preferentially interact with the water.
|
||||
#
|
||||
# Why is this necessary?
|
||||
# Shouldn't attraction between lipid tails and the protein create
|
||||
# an effective force which brings the hydrophilic beads together?
|
||||
# (similar to the hydrophobic effect, but in reverse?).
|
||||
# Answer:
|
||||
# Unlike an aqueous environment (~zero pressure, or +1atm), there is
|
||||
# a large negative pressure in the interior of some bilayer membrane
|
||||
# models (such as this one). Without some kind of direct attraction
|
||||
# between interior residues, the protein will get pulled apart.
|
||||
# (Perhaps the attractive force I am using is too strong?)
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
# Finally, we must combine the two force-field styles which were used for
|
||||
# the coarse-grained lipid and protein. To do that, we write one last time
|
||||
# to the "In Init" section. When reading the "Init" section LAMMPS will
|
||||
# read these commands last and this will override any earlier settings.
|
||||
|
||||
write_once("In Init") {
|
||||
# -- These styles override earlier settings --
|
||||
units real
|
||||
atom_style full
|
||||
# (Hybrid force field styles were used for portability.)
|
||||
bond_style hybrid harmonic
|
||||
angle_style hybrid cosine/delta harmonic
|
||||
dihedral_style hybrid fourier
|
||||
improper_style none
|
||||
pair_style hybrid table linear 1130 lj/charmm/coul/charmm/inter es4k4l 14.5 15
|
||||
pair_modify mix arithmetic
|
||||
special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds"
|
||||
}
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,35 @@
|
|||
# -------- 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
|
||||
|
|
@ -0,0 +1,60 @@
|
|||
# -------- REQUIREMENTS: ---------
|
||||
# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC")
|
||||
# http://lammps.sandia.gov/doc/Section_start.html#start_3
|
||||
# 2) It also may require additional features and bug fixes for LAMMPS.
|
||||
# So, after typing "make yes-user-misc" in to the shell, ...
|
||||
# be sure to download and copy the "additional_lammps_code" from
|
||||
# http://moltemplate.org (upper-left corner menu)
|
||||
# 3) Unpack it
|
||||
# 4) copy the .cpp and .h files to the src folding of your lammps installation.
|
||||
# 5) Compile LAMMPS.
|
||||
#
|
||||
# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style"
|
||||
# then you made a mistake in the instructions above.
|
||||
#
|
||||
|
||||
# -- Init Section --
|
||||
|
||||
include system.in.init
|
||||
|
||||
# -- Atom Definition Section --
|
||||
|
||||
read_data system.data
|
||||
|
||||
# -- Settings Section --
|
||||
|
||||
include system.in.settings
|
||||
|
||||
# -- Run Section --
|
||||
|
||||
#minimize 1.0e-5 1.0e-7 500 2000
|
||||
|
||||
timestep 10.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs
|
||||
dump 1 all custom 10000 traj_npt.lammpstrj id mol type x y z ix iy iz
|
||||
|
||||
|
||||
thermo_style custom step temp pe etotal vol epair ebond eangle
|
||||
thermo 1000 # time interval for printing out "thermo" data
|
||||
|
||||
|
||||
fix fxlan all langevin 300.0 300.0 120 48279
|
||||
fix fxnph all nph x 0 0 1000 y 0 0 1000 couple xy
|
||||
|
||||
|
||||
# Note: The temperature 300.0 K corresponds to 0.907033536873*epsilon
|
||||
# (for the "epsilon" used by the coarse-grained lipid), and
|
||||
# to 0.33*epsilon (for the "epsilon" used in the coarse-grained protein)
|
||||
# Note: The langevin damping parameter "120" corresponds to
|
||||
# the 0.12ps damping time used in Watson et. al JCP 2011.
|
||||
# Note: We maintain the system system at constant (zero) tention
|
||||
# using a barostat damping parameter Pdamp=1000 ("0 0 1000")
|
||||
|
||||
|
||||
# optional (not sure if this helps):
|
||||
# balance x uniform y uniform
|
||||
|
||||
|
||||
run 10000000
|
||||
|
||||
write_restart system_after_npt.rst
|
||||
|
||||
|
|
@ -0,0 +1,67 @@
|
|||
# -------- REQUIREMENTS: ---------
|
||||
# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC")
|
||||
# http://lammps.sandia.gov/doc/Section_start.html#start_3
|
||||
# 2) It also may require additional features and bug fixes for LAMMPS.
|
||||
# So, after typing "make yes-user-misc" in to the shell, ...
|
||||
# be sure to download and copy the "additional_lammps_code" from
|
||||
# http://moltemplate.org (upper-left corner menu)
|
||||
# 3) Unpack it
|
||||
# 4) copy the .cpp and .h files to the src folding of your lammps installation.
|
||||
# 5) Compile LAMMPS.
|
||||
#
|
||||
# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style"
|
||||
# then you made a mistake in the instructions above.
|
||||
#
|
||||
# ------------------------------- Initialization Section --------------------
|
||||
|
||||
include system.in.init
|
||||
|
||||
# ------------------------------- Atom Definition Section -------------------
|
||||
|
||||
|
||||
# Normally, I would minimize the system and equilibrate the system at constant
|
||||
# pressure and temperature beforehand. If you run lammps with "run.in.npt",
|
||||
# it will generate a restart file "system_after_npt.rst" with reasonable
|
||||
# coordinates at that temperature and pressure. Then we could load it now:
|
||||
#
|
||||
#read_restart system_after_npt.rst
|
||||
#
|
||||
# Unfortunately the LAMMPS "read_restart" command has been undependable over
|
||||
# the past year (2012), and I feel it is safer to remove it from the examples.
|
||||
# Instead, for this example, I just read the raw coordinates generated by
|
||||
# moltemplate (and the default volume). (I get fewer questions this way.)
|
||||
# However you should never run any liquid simulations at constant volume without
|
||||
# pressure equilibration first. Hopefully in the future "read_restart" will
|
||||
# work. Until then, try "read_dump", "dump2data.py", or "restart2data".
|
||||
|
||||
read_data system.data
|
||||
|
||||
# ------------------------------- Settings Section --------------------------
|
||||
|
||||
include system.in.settings
|
||||
|
||||
# ------------------------------- Run Section -------------------------------
|
||||
|
||||
|
||||
timestep 10.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs
|
||||
dump 1 all custom 10000 traj_nvt.lammpstrj id mol type x y z ix iy iz
|
||||
|
||||
|
||||
thermo_style custom step temp pe etotal vol epair ebond eangle
|
||||
thermo 1000 # time interval for printing out "thermo" data
|
||||
|
||||
|
||||
fix fxlan all langevin 300.0 300.0 120 48279
|
||||
fix fxnve all nve
|
||||
|
||||
# Note: The energy scale "epsilon" = 2.75kJ/mole = 330.7485200981 Kelvin*kB.
|
||||
# So a temperature of 300.0 Kelvin corresponds to 0.907033536873*epsilon.
|
||||
# Note: The langevin damping parameter "120" corresponds to
|
||||
# the 0.12ps damping time used in Watson et. al JCP 2011.
|
||||
|
||||
#restart 500000
|
||||
|
||||
run 10000000
|
||||
|
||||
write_restart system_after_nvt.rst
|
||||
|
||||
|
|
@ -0,0 +1,33 @@
|
|||
Note:
|
||||
This example may require additional features to be added to LAMMPS.
|
||||
If LAMMPS complains about an "Invalid pair_style", then copy the code
|
||||
in the "additional_lammps_code" directory into your LAMMPS "src" directory
|
||||
and recompile LAMMPS.
|
||||
|
||||
----- Description --------
|
||||
|
||||
This example contains an implementation of the DPPC lipid bilayer described in:
|
||||
G. Brannigan, P.F. Philips, and F.L.H. Brown,
|
||||
Physical Review E, Vol 72, 011915 (2005)
|
||||
and:
|
||||
M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown
|
||||
J. Chem. Phys. 135, 244701 (2011)
|
||||
|
||||
As in Watson(JCP 2011), rigid bond-length constraints
|
||||
have been replaced by harmonic bonds.
|
||||
|
||||
A truncated version of this lipid (named "DLPC") has also been added.
|
||||
Unlike the original "DPPC" molecule model, "DLPC" has not been carefully
|
||||
parameterized to reproduce the correct behavior in a lipid bilayer mixture.
|
||||
|
||||
|
||||
-------------
|
||||
|
||||
Instructions on how to build LAMMPS input files and
|
||||
run a short simulation are provided in other README files.
|
||||
|
||||
step 1)
|
||||
README_setup.sh
|
||||
|
||||
step2)
|
||||
README_run.sh
|
||||
|
|
@ -0,0 +1,33 @@
|
|||
# --- Running LAMMPS ---
|
||||
# -- Prerequisites: --
|
||||
# The "run.in.nvt" file is a LAMMPS input script containing
|
||||
# references to the input scripts and data files
|
||||
# you hopefully have created earlier with moltemplate.sh:
|
||||
# system.in.init, system.in.settings, system.data, and table_int.dat
|
||||
# If not, carry out the instructions in "README_setup.sh".
|
||||
#
|
||||
# -- Instructions: --
|
||||
# If "lmp_linux" is the name of the command you use to invoke lammps,
|
||||
# then you would run lammps on these files this way:
|
||||
|
||||
|
||||
lmp_linux -i run.in.npt # Run a simulation at constant pressure (tension)
|
||||
|
||||
#or
|
||||
|
||||
lmp_linux -i run.in.nvt # Run a simulation at constant volume
|
||||
|
||||
#(Note: The constant volume simulation lacks pressure equilibration. These are
|
||||
# completely separate simulations. The results of the constant pressure
|
||||
# simulation are ignored when beginning the simulation at constant volume.
|
||||
# This can be fixed. Read "run.in.nvt" for equilibration instructions.)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
# If you have compiled the MPI version of lammps, you can run lammps in parallel
|
||||
#mpirun -np 4 lmp_linux -i run.in.npt
|
||||
#or
|
||||
#mpirun -np 4 lmp_linux -i run.in.nvt
|
||||
# (assuming you have 4 processors available)
|
||||
|
|
@ -0,0 +1,28 @@
|
|||
# Use these commands to generate the LAMMPS input script and data file
|
||||
# (and other auxilliary files):
|
||||
|
||||
|
||||
# Create LAMMPS input files this way:
|
||||
cd moltemplate_files
|
||||
|
||||
# run moltemplate
|
||||
|
||||
moltemplate.sh system.lt
|
||||
|
||||
# This will generate various files with names ending in *.in* and *.data.
|
||||
# These files are the input files directly read by LAMMPS. Move them to
|
||||
# the parent directory (or wherever you plan to run the simulation).
|
||||
|
||||
mv -f system.in* system.data ../
|
||||
|
||||
# The "table_int.dat" file contains tabular data for the lipid INT-INT atom
|
||||
# 1/r^2 interaction. We need it too. (This slows down the simulation by x2,
|
||||
# so I might look for a way to get rid of it later.)
|
||||
cp -f table_int.dat ../
|
||||
|
||||
# Optional:
|
||||
# The "./output_ttree/" directory is full of temporary files generated by
|
||||
# moltemplate. They can be useful for debugging, but are usually thrown away.
|
||||
rm -rf output_ttree/
|
||||
|
||||
cd ../
|
||||
|
|
@ -0,0 +1,87 @@
|
|||
|
||||
------- To view a lammps trajectory in VMD --------
|
||||
|
||||
|
||||
1) Build a PSF file for use in viewing with VMD.
|
||||
|
||||
This step works with VMD 1.9 and topotools 1.2.
|
||||
(Older versions, like VMD 1.8.6, don't support this.)
|
||||
|
||||
|
||||
a) Start VMD
|
||||
b) Menu Extensions->Tk Console
|
||||
c) Enter:
|
||||
|
||||
(I assume that the the DATA file is called "system.data")
|
||||
|
||||
topo readlammpsdata system.data full
|
||||
animate write psf system.psf
|
||||
|
||||
2)
|
||||
|
||||
Later, to Load a trajectory in VMD:
|
||||
|
||||
Start VMD
|
||||
Select menu: File->New Molecule
|
||||
-Browse to select the PSF file you created above, and load it.
|
||||
(Don't close the window yet.)
|
||||
-Browse to select the trajectory file.
|
||||
If necessary, for "file type" select: "LAMMPS Trajectory"
|
||||
Load it.
|
||||
|
||||
---- A note on trajectory format: -----
|
||||
If the trajectory is a DUMP file, then make sure the it contains the
|
||||
information you need for pbctools (see below. I've been using this
|
||||
command in my LAMMPS scripts to create the trajectories:
|
||||
|
||||
dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
|
||||
|
||||
It's a good idea to use an atom_style which supports molecule-ID numbers
|
||||
so that you can assign a molecule-ID number to each atom. (I think this
|
||||
is needed to wrap atom coordinates without breaking molecules in half.)
|
||||
|
||||
Of course, you don't have to save your trajectories in DUMP format,
|
||||
(other formats like DCD work fine) I just mention dump files
|
||||
because these are the files I'm familiar with.
|
||||
|
||||
3) ----- Wrap the coordinates to the unit cell
|
||||
(without cutting the molecules in half)
|
||||
|
||||
a) Start VMD
|
||||
b) Load the trajectory in VMD (see above)
|
||||
c) Menu Extensions->Tk Console
|
||||
d) Try entering these commands:
|
||||
|
||||
pbc wrap -compound res -all
|
||||
pbc box
|
||||
|
||||
----- Optional ----
|
||||
Sometimes the solvent or membrane obscures the view of the solute.
|
||||
It can help to shift the location of the periodic boundary box
|
||||
To shift the box in the y direction (for example) do this:
|
||||
|
||||
pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
|
||||
pbc box -shiftcenterrel {0.0 0.15 0.0}
|
||||
|
||||
Distances are measured in units of box-length fractions, not Angstroms.
|
||||
|
||||
Alternately if you have a solute whose atoms are all of type 1,
|
||||
then you can also try this to center the box around it:
|
||||
|
||||
pbc wrap -sel type=1 -all -centersel type=2 -center com
|
||||
|
||||
4)
|
||||
You should check if your periodic boundary conditions are too small.
|
||||
To do that:
|
||||
select Graphics->Representations menu option
|
||||
click on the "Periodic" tab, and
|
||||
click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
|
||||
|
||||
5) Optional: If you like, change the atom types in the PSF file so
|
||||
that VMD recognizes the atom types, use something like:
|
||||
|
||||
sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
|
||||
sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
|
||||
sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
|
||||
|
||||
(If you do this, it might effect step 2 above.)
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 4.8 KiB |
Binary file not shown.
|
After Width: | Height: | Size: 57 KiB |
Binary file not shown.
|
After Width: | Height: | Size: 36 KiB |
Binary file not shown.
|
After Width: | Height: | Size: 61 KiB |
Binary file not shown.
|
After Width: | Height: | Size: 5.7 KiB |
|
|
@ -0,0 +1,191 @@
|
|||
# Note:
|
||||
#
|
||||
# This example may require additional features to be added to LAMMPS. If
|
||||
# LAMMPS complains about an "Invalid pair_style", then download copy the
|
||||
# "additional_lammps_code" from moltemplate.org, unpack it into your LAMMPS
|
||||
# "src" directory and recompile LAMMPS.
|
||||
#
|
||||
# -------- Description --------
|
||||
#
|
||||
# This example contains an implementation of the DPPC lipid bilayer described in
|
||||
# G. Brannigan, P.F. Philips, and F.L.H. Brown,
|
||||
# Physical Review E, Vol 72, 011915 (2005)
|
||||
# and:
|
||||
# M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown
|
||||
# J. Chem. Phys. 135, 244701 (2011)
|
||||
#
|
||||
# As in Watson(JCP 2011), rigid bond-length constraints have been replaced
|
||||
# by harmonic bonds.
|
||||
#
|
||||
# --- DLPC lipids ---
|
||||
# A truncated version of the DPPC lipid (named "DLPC") has also been added.
|
||||
# Unlike the original "DPPC" molecule model, "DLPC" has not been carefully
|
||||
# parameterized to reproduce the correct behavior in a lipid bilayer/mixture.
|
||||
# (You may need to stiffen the bond-angle forces to make it behave correctly,
|
||||
# but I did not do this here.)
|
||||
#
|
||||
# Units:
|
||||
#
|
||||
# The "epsilon" parameter in their model is approximately 2.75 kJ/mole
|
||||
# ( = 0.657265774378585 kCal/mole, using 1kCal=4.184kJ)
|
||||
# The "sigma" parameter corresponds to 7.5 angstroms.
|
||||
#
|
||||
#
|
||||
# The new DLPC model is a truncated version of DPPC,
|
||||
# (Its behaviour has not been rigorously tested.)
|
||||
|
||||
|
||||
CGLipidBr2005 {
|
||||
|
||||
|
||||
write_once("In Init") {
|
||||
# -- Default styles for "CGLipidBr2005" --
|
||||
units real
|
||||
atom_style full
|
||||
# (Hybrid force field styles were used for portability.)
|
||||
bond_style hybrid harmonic
|
||||
angle_style hybrid cosine/delta
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
pair_style hybrid table linear 1001 &
|
||||
lj/charmm/coul/charmm/inter es4k4l 14.5 15
|
||||
pair_modify mix arithmetic
|
||||
special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds"
|
||||
|
||||
neighbor 2.0 multi # <- perhaps unnecessary
|
||||
communicate multi # <- perhaps unnecessary
|
||||
}
|
||||
|
||||
|
||||
DPPC {
|
||||
write("Data Atoms") {
|
||||
$atom:h $mol:. @atom:head 0.0 0.00 0.00 33.75 # DPPC head atom
|
||||
$atom:i $mol:. @atom:../int 0.0 -1.00 0.00 26.25
|
||||
$atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 18.75
|
||||
$atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 11.25
|
||||
$atom:t3 $mol:. @atom:../tail 0.0 1.00 0.00 3.75
|
||||
}
|
||||
write("Data Bonds") {
|
||||
$bond:b1 @bond:../backbone $atom:h $atom:i
|
||||
$bond:b2 @bond:../backbone $atom:i $atom:t1
|
||||
$bond:b3 @bond:../backbone $atom:t1 $atom:t2
|
||||
$bond:b4 @bond:../backbone $atom:t2 $atom:t3
|
||||
}
|
||||
write("Data Angles") {
|
||||
$angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1
|
||||
$angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2
|
||||
$angle:a3 @angle:../backbone $atom:t1 $atom:t2 $atom:t3
|
||||
}
|
||||
|
||||
# Define properties of the local (lipid-specific) atom:head type atom:
|
||||
write_once("Data Masses") {
|
||||
@atom:head 200.0
|
||||
}
|
||||
write_once("In Settings") {
|
||||
pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
}
|
||||
|
||||
} #DPPC
|
||||
|
||||
|
||||
DLPC {
|
||||
write("Data Atoms") {
|
||||
$atom:h $mol:. @atom:head 0.0 0.00 0.00 30.00 # DLPC head atom
|
||||
$atom:i $mol:. @atom:../int 0.0 -1.00 0.00 22.50
|
||||
$atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 15.00
|
||||
$atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 7.50
|
||||
}
|
||||
write("Data Bonds") {
|
||||
$bond:b1 @bond:../backbone $atom:h $atom:i
|
||||
$bond:b2 @bond:../backbone $atom:i $atom:t1
|
||||
$bond:b3 @bond:../backbone $atom:t1 $atom:t2
|
||||
}
|
||||
write("Data Angles") {
|
||||
$angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1
|
||||
$angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2
|
||||
}
|
||||
# Define properties of the local (lipid-specific) atom:head type atom:
|
||||
write_once("Data Masses") {
|
||||
@atom:head 200.0
|
||||
}
|
||||
write_once("In Settings") {
|
||||
pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
}
|
||||
} #DLPC
|
||||
|
||||
|
||||
# Particles shared by all lipid types
|
||||
write_once("Data Masses") {
|
||||
@atom:int 200.0
|
||||
@atom:tail 200.0
|
||||
@atom:head 200.0 #<- Default head type. We may override it later.
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
# -- Default settings/parameters for "CGLipidBr2005" --
|
||||
# (Hybrid bond & angle styles were used for portability.)
|
||||
|
||||
# As in Watson(JCP 2011), rigid bond-length constraints
|
||||
# have been replaced by harmonic bonds.
|
||||
# The k_theta parameter should lie in between 5*epsilon and 10*epsilon.
|
||||
bond_coeff @bond:backbone harmonic 116.847 7.5 #<--2*5000*eps/sig^2
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
angle_coeff @angle:backbone cosine/delta 4.60086042 180 #<-- 7*eps
|
||||
#angle_coeff @angle:backbone cosine/delta 6.57265774 180 #<-- 10*eps
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
|
||||
# The interaction of "atom:int" with other "atom:int" atoms is given by
|
||||
# epsilon*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2), shifted and cutoff at
|
||||
# r=3*sigma. This was implemented using pair_style table.
|
||||
# Unfortunately, mixing lj/charmm and "table" pair styles in the same
|
||||
# simulation is very inneficient.
|
||||
|
||||
pair_coeff @atom:int @atom:int table table_int.dat INT
|
||||
|
||||
# The interaction of tail beads with eachother is given by the formula below
|
||||
# and with other atoms ...using Lorenz-Berthelot and "repulsive wins" rules:
|
||||
# epsilon*(0.4*(sigma/r)^12 - 1.0*(sigma/r)^6),
|
||||
pair_coeff @atom:tail @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1
|
||||
pair_coeff @atom:int @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1
|
||||
|
||||
# The interaction of head beads which all other beads is given by:
|
||||
# epsilon*(0.4*(sigma/r)^12 - 0.0*(sigma/r)^6),
|
||||
|
||||
pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
pair_coeff @atom:int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
|
||||
|
||||
} # write_once("In Settings")
|
||||
|
||||
# Note: I divided epsilon by 4 to get "0.1643" because we are using the
|
||||
# "es4k4l" coeffstyle, corresponding to U(r)=eps(4*K*(s/r)^12 + 4*L*(s/r)^6)
|
||||
# (The "es4k4l" coeffstyle is the default.) Using this convention makes it
|
||||
# easier to mix this coarse-grained lipid model with other molecular models.
|
||||
|
||||
|
||||
|
||||
} # CGLipidBr2005
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
# Note: This example has not been optimized for speed.
|
||||
#
|
||||
# Unfortunately, using both lj/charmm and "table" pair styles in the same
|
||||
# simulation seems to be very inneficient. (The simulation is twice as slow
|
||||
# as using only the "lj/charmm" pair styles for every pairwise interaction,
|
||||
# ...and about 25% slower than using "table" for every pairwise interaction.
|
||||
# However the lennard-jones pair styles support mixing, so we use them to
|
||||
# make it easier to run these molecules with other molecules which don't use
|
||||
# pair_table. I felt that portability was worth the extra 25% slow down.)
|
||||
|
||||
|
|
@ -0,0 +1,34 @@
|
|||
#!/usr/bin/env python
|
||||
|
||||
# Calculate a table of pairwise energies and forces between "INT" atoms
|
||||
# in the lipid membrane model described in
|
||||
# Brannigan et al, Phys Rev E, 72, 011915 (2005)
|
||||
# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2)
|
||||
# However it is truncated at rc2 = 22.5 (shifted upwards to maintain continuity)
|
||||
|
||||
# The previous version included the repulsive core term
|
||||
def U(r, eps, sigma):
|
||||
return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r))
|
||||
def F(r, eps, sigma):
|
||||
return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r))
|
||||
# We don't want to do that. Instead compute the core repulsion using a
|
||||
# different pair_style and add the attractive term on top of it using the table.
|
||||
# This way it the core repulsion acts as a default interaction with other atom
|
||||
# types (using the new repulsive mixing rules).
|
||||
|
||||
epsilon = 2.75/4.184 # kCal/mole
|
||||
sigma = 7.5
|
||||
Rmin = 0.02
|
||||
Rmax = 22.6
|
||||
rcut = 22.5
|
||||
N = 1130
|
||||
|
||||
for i in range(0,N):
|
||||
r = Rmin + i*(Rmax-Rmin)/(N-1)
|
||||
U_r = U(r, epsilon, sigma) - U(rcut, epsilon, sigma)
|
||||
F_r = F(r, epsilon, sigma)
|
||||
if r > rcut:
|
||||
U_r = 0.0
|
||||
F_r = 0.0
|
||||
print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))
|
||||
|
||||
|
|
@ -0,0 +1,70 @@
|
|||
#!/usr/bin/env python
|
||||
|
||||
# Calculate a table of pairwise energies and forces between "INT" atoms
|
||||
# in the lipid membrane model described in
|
||||
# Brannigan et al, Phys Rev E, 72, 011915 (2005)
|
||||
# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2)
|
||||
# I realized later this is not what we want because although energy is conserved
|
||||
# all enrgies are shifted with respect to energies used in the Brannigan paper
|
||||
# (by 0.27 kCal/mole) and the later Watson JCP 2011 paper (by 0.224 kCal/mole).
|
||||
# (So don't use this.)
|
||||
|
||||
# Calculate and print a
|
||||
|
||||
def S(r, rc1, rc2, derivative=False):
|
||||
"""
|
||||
Calculate the switching function S(r) which decays continuously
|
||||
between 1 and 0 in the range from rc1 to rc2 (rc2>rc1):
|
||||
S(r) = (rc2^2 - r^2)^2 * (rc2^2 + 2*r^2 - 3*rc1^2) / (rc2^2-rc1^2)^3
|
||||
I'm using the same smoothing/switching cutoff function used by the CHARMM
|
||||
force-fields. (I'm even using the same code to implement it, taken
|
||||
from lammps charmm/coul/charmm pair style, rewritten in python.)
|
||||
|
||||
"""
|
||||
assert(rc2>rc1)
|
||||
rsq = r*r
|
||||
rc1sq = rc1*rc1
|
||||
rc2sq = rc2*rc2
|
||||
denom_lj_inv = (1.0 / ((rc2sq-rc1sq)*
|
||||
(rc2sq-rc1sq)*
|
||||
(rc2sq-rc1sq)))
|
||||
if rsq > rc2sq:
|
||||
return 0.0
|
||||
elif rsq < rc1sq:
|
||||
if derivative:
|
||||
return 0.0
|
||||
else:
|
||||
return 1.0
|
||||
else:
|
||||
rc2sq_minus_rsq = (rc2sq - rsq)
|
||||
rc2sq_minus_rsq_sq = rc2sq_minus_rsq * rc2sq_minus_rsq
|
||||
if derivative:
|
||||
return (12.0 * rsq * rc2sq_minus_rsq * (rsq-rc1sq) * denom_lj_inv)
|
||||
else:
|
||||
return (rc2sq_minus_rsq_sq *
|
||||
(rc2sq + 2.0*rsq - 3.0*rc1sq) * denom_lj_inv)
|
||||
|
||||
|
||||
def U(r, eps, sigma):
|
||||
return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r))
|
||||
|
||||
def F(r, eps, sigma):
|
||||
return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r))
|
||||
|
||||
epsilon = 2.75/4.184 # kCal/mole
|
||||
sigma = 7.5
|
||||
Rmin = 0.02
|
||||
Rmax = 22.6
|
||||
Rc1 = 22.0
|
||||
Rc2 = 22.5
|
||||
N = 1130
|
||||
|
||||
for i in range(0,N):
|
||||
r = Rmin + i*(Rmax-Rmin)/(N-1)
|
||||
U_r = U(r, epsilon, sigma)
|
||||
F_r = F(r, epsilon, sigma)
|
||||
# Multiply U(r) & F(r) by the smoothing/switch function
|
||||
U_r = U_r * S(r, Rc1, Rc2)
|
||||
F_r = U_r * S(r, Rc1, Rc2, True) + F_r * S(r, Rc1, Rc2, False)
|
||||
print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))
|
||||
|
||||
|
|
@ -0,0 +1,94 @@
|
|||
# Description:
|
||||
|
||||
# This constructs a bilayer constructed from coarse-grained DPPC lipids
|
||||
# (implicit solvent). The DPPC lipid model is described here:
|
||||
# G. Brannigan, P.F. Philips, and F.L.H. Brown,
|
||||
# Physical Review E, Vol 72, 011915 (2005)
|
||||
#
|
||||
# NOTE: There is an example of a 50%/50% DPPC & DLPC mixture
|
||||
# in the "membrane+protein" and "vesicle" examples.
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
import "CGLipidBr2005Orig.lt"
|
||||
|
||||
using namespace CGLipidBr2005
|
||||
|
||||
lipids = new DPPC [32].move(7.5, 0, 0)
|
||||
[37].move(3.75, 6.49519, 0)
|
||||
[2].rot(180, 1, 0, 0)
|
||||
|
||||
|
||||
# Move the lipds up to the center of the box
|
||||
lipids[*][*][*].move(0,0,75.0)
|
||||
|
||||
|
||||
# Although this patch of lipids is not square or rectangular, (it looks
|
||||
# like a parallelogram), this is no longer the case after rectangular
|
||||
# periodic boundary conditions are applied. We apply them below:
|
||||
# width: 240 = 32*7.5
|
||||
# height: 240.322 = 37*6.49519
|
||||
|
||||
write_once("Data Boundary") {
|
||||
0 240 xlo xhi
|
||||
0 240.322 ylo yhi
|
||||
0 150.0 zlo zhi
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
# -------------- File ends here. Only comments below.-------------------
|
||||
|
||||
# ------------------------------------
|
||||
# ------------- COMMENTS: ------------
|
||||
# ------------------------------------
|
||||
#
|
||||
# A note on geometry:
|
||||
# We want to create a bilayer arranged in a hexagonal lattice consisting of
|
||||
# 32 rows (each row is aligned with the x-axis)
|
||||
# 37 columns (aligned at a 60 degree angle from the x axis)
|
||||
# The lattice spacing is 8.0 Angstroms ( ~= 0.95*sigma*2^(1/6), where sigma=7.5)
|
||||
# When wrapped onto a rectangular box, the dimensions of the system are:
|
||||
# 32 * 7.5 Angstroms in the X direction
|
||||
# 37 * 7.5*sqrt(3)/2 Angstroms in the Y direction
|
||||
# ------------------------------------
|
||||
#
|
||||
# Below I show simple ways to create a lipid bilayer:
|
||||
#
|
||||
# 1) If you just want to make lipid bilayer out of DPPC,
|
||||
# without specifying the location of each lipid, you could use this syntax:
|
||||
# lipids = new DPPC [32][37][2] # 3-D array
|
||||
# Later you can load in the coordinates of the lipds from a PDB file.
|
||||
# Alternately you could also use a 1-dimensional array:
|
||||
# lipids = new DPPC [2368] # 1-D array. Note: 2368 = 32 x 37 x 2
|
||||
# It does not matter as long as the number of lipids is correct.
|
||||
# Multidimensional arrays are only useful if you plan to apply independent
|
||||
# coordinate transformations to each row and column and monolayer. See below:
|
||||
#
|
||||
# 2) Instead of loading a PDB file later, we can directly specify the location
|
||||
# of each DPPC lipid in the LT file itself. For lipid bilayers, this is
|
||||
# easy, because the bilayer structure resembles 2 planar lattices.
|
||||
# We can use "move" commands to place each lipid, and the "rot" command
|
||||
# to turn the lipids in one of the monolayers upside down.
|
||||
#
|
||||
# lipids = new DPPC [32].move(7.5, 0, 0)
|
||||
# [37].move(3.75, 6.49519, 0)
|
||||
# [2].rot(180, 1, 0, 0)
|
||||
#
|
||||
# 3) If you want to create a bilayer from a mixture of DPPC and DLPC, you must
|
||||
# replace "DPPC" in the command above with random([DPPC,DLPC],[0.5,0.5],12345)
|
||||
# Here "0.5,0.5" are the probabilities for each molecule type, and "12345"
|
||||
# is an optional random seed.
|
||||
# lipids = new random([DPPC,DLPC], [0.5,0.5], 12345)
|
||||
# [32].move(7.5, 0, 0)
|
||||
# [37].move(3.75, 6.49519, 0)
|
||||
# [2].rot(180, 1, 0, 0)
|
||||
#
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,28 @@
|
|||
# -- Init section --
|
||||
|
||||
include system.in.init
|
||||
|
||||
# -- Atom definition section --
|
||||
|
||||
read_data system.data
|
||||
|
||||
# -- Settings Section --
|
||||
|
||||
include system.in.settings
|
||||
|
||||
# Optional: Make sure the pairwise energies look reasonable:
|
||||
#pair_write 2 2 1001 r 2.6 16.0 test_tail-tail.dat t-t 0 0
|
||||
#pair_write 2 3 1001 r 2.6 16.0 test_tail-head.dat t-h 0 0
|
||||
#pair_write 1 2 1001 r 2.6 16.0 test_int-tail.dat i-t 0 0
|
||||
#pair_write 1 1 2573 r 2.6 16.0 test_int-int.dat i-i 0 0
|
||||
#pair_write 1 3 1001 r 2.6 16.0 test_int-head.dat i-h 0 0
|
||||
#pair_write 3 3 1001 r 2.6 16.0 test_head-head.dat h-h 0 0
|
||||
|
||||
|
||||
# -- Run section --
|
||||
|
||||
dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz
|
||||
|
||||
minimize 1.0e-5 1.0e-7 500 2000
|
||||
|
||||
write_restart system_after_min.rst
|
||||
|
|
@ -0,0 +1,57 @@
|
|||
# -------- REQUIREMENTS: ---------
|
||||
# 1) This example may require additional features and bug fixes for LAMMPS.
|
||||
# Be sure to download and copy the "additional_lammps_code" from
|
||||
# http://moltemplate.org (upper-left corner menu)
|
||||
# 2) Unpack it
|
||||
# 3) copy the .cpp and .h files to the src folding of your lammps installation.
|
||||
# 4) Compile LAMMPS.
|
||||
#
|
||||
# (If LAMMPS complains about an "Invalid pair_style"
|
||||
# then you made a mistake in the instructions above.)
|
||||
#
|
||||
|
||||
# -- Init Section --
|
||||
|
||||
include system.in.init
|
||||
|
||||
# -- Atom Definition Section --
|
||||
|
||||
read_data system.data
|
||||
|
||||
# -- Settings Section --
|
||||
|
||||
include system.in.settings
|
||||
|
||||
# -- Run Section --
|
||||
|
||||
|
||||
timestep 6.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs
|
||||
dump 1 all custom 5000 traj_npt.lammpstrj id mol type x y z ix iy iz
|
||||
|
||||
|
||||
thermo_style custom step temp pe etotal vol epair ebond eangle
|
||||
thermo 1000 # time interval for printing out "thermo" data
|
||||
|
||||
|
||||
fix fxlan all langevin 300.0 300.0 120 48279
|
||||
fix fxnph all nph x 0 0 1000 y 0 0 1000 couple xy
|
||||
|
||||
|
||||
# Note: The temperature 300.0 K corresponds to 0.907033536873*epsilon
|
||||
# for the "epsilon" used by the coarse-grained lipid.
|
||||
# Note: The langevin damping parameter "120" corresponds to
|
||||
# the 0.12ps damping time used in Watson et. al JCP 2011.
|
||||
# Note: We maintain the system system at constant (zero) tention
|
||||
# using a barostat damping parameter Pdamp=1000 ("0 0 1000")
|
||||
|
||||
|
||||
# optional (not sure if this helps):
|
||||
# balance x uniform y uniform
|
||||
|
||||
|
||||
#restart 1000000
|
||||
|
||||
run 2000000
|
||||
|
||||
write_restart system_after_npt.rst
|
||||
|
||||
|
|
@ -0,0 +1,53 @@
|
|||
# ------------------------------- Initialization Section --------------------
|
||||
|
||||
include system.in.init
|
||||
|
||||
# ------------------------------- Atom Definition Section -------------------
|
||||
|
||||
|
||||
# Normally, I would minimize the system and equilibrate the system at constant
|
||||
# pressure and temperature beforehand. If you run lammps with "run.in.npt",
|
||||
# it will generate a restart file "system_after_npt.rst" with reasonable
|
||||
# coordinates at that temperature and pressure. Then we could load it now:
|
||||
#
|
||||
#read_restart system_after_npt.rst
|
||||
#
|
||||
# Unfortunately the LAMMPS "read_restart" command has been undependable over
|
||||
# the past year (2012), and I feel it is safer to remove it from the examples.
|
||||
# Instead, for this example, I just read the raw coordinates generated by
|
||||
# moltemplate (and the default volume). (I get fewer questions this way.)
|
||||
# However you should never run any liquid simulations at constant volume without
|
||||
# pressure equilibration first. Hopefully in the future "read_restart" will
|
||||
# work. Until then, try "read_dump", "dump2data.py", or "restart2data".
|
||||
|
||||
read_data system.data
|
||||
|
||||
# ------------------------------- Settings Section --------------------------
|
||||
|
||||
include system.in.settings
|
||||
|
||||
# ------------------------------- Run Section -------------------------------
|
||||
|
||||
|
||||
timestep 6.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs
|
||||
dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz
|
||||
|
||||
|
||||
thermo_style custom step temp pe etotal vol epair ebond eangle
|
||||
thermo 1000 # time interval for printing out "thermo" data
|
||||
|
||||
|
||||
fix fxlan all langevin 300.0 300.0 120 48279
|
||||
fix fxnve all nve
|
||||
|
||||
# Note: The energy scale "epsilon" = 2.75kJ/mole = 330.7485200981 Kelvin*kB.
|
||||
# So a temperature of 300.0 Kelvin corresponds to 0.907033536873*epsilon.
|
||||
# Note: The langevin damping parameter "120" corresponds to
|
||||
# the 0.12ps damping time used in Watson et. al JCP 2011.
|
||||
|
||||
#restart 1000000
|
||||
|
||||
run 1000000
|
||||
|
||||
write_restart system_after_nvt.rst
|
||||
|
||||
|
|
@ -0,0 +1,33 @@
|
|||
# This directory contains examples of how to run a short simulation of a
|
||||
# coarse-grained protein-like polymer, folding in the presence and absence of
|
||||
# a chaperone (modeled as an attractive or repulsie spherical shell).
|
||||
#
|
||||
# The protein models and the chaperone models are described and used here:
|
||||
# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
|
||||
# (http://www.pnas.org/content/101/36/13192)
|
||||
# ...and also here:
|
||||
# AI Jewett and J-E Shea, J. Mol. Biol, Vol 363(5), (2006)
|
||||
#
|
||||
# (In the "frustrated+minichaperone" directory, the protein is
|
||||
# placed outside the chaperone sphere, as opposed to inside.)
|
||||
#
|
||||
# -------- REQUIREMENTS: ---------
|
||||
# 1) These examples require the "USER-MISC" package. (Use "make yes-USER-MISC")
|
||||
# http://lammps.sandia.gov/doc/Section_start.html#start_3
|
||||
# 2) They also may require additional features and bug fixes for LAMMPS.
|
||||
# be sure to download and copy the "additional_lammps_code" from
|
||||
# http://moltemplate.org (upper-left corner menu)
|
||||
# 3) Unpack it
|
||||
# 4) copy the .cpp and .h files to the src folding of your lammps installation.
|
||||
# 5) Compile LAMMPS.
|
||||
#
|
||||
|
||||
-------------
|
||||
Instructions on how to build LAMMPS input files and
|
||||
run a short simulation are provided in other README files in each directory.
|
||||
|
||||
step 1)
|
||||
README_setup.sh
|
||||
|
||||
step2)
|
||||
README_run.sh
|
||||
|
|
@ -0,0 +1,32 @@
|
|||
# This directory demonstrates how to run a long simulation of
|
||||
# the "frustrated" coarse-grained protein confined in a frustrated
|
||||
# coarse-grained chaperonin (R=6, h=0.475) as described in:
|
||||
# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
|
||||
# (http://www.pnas.org/content/101/36/13192)
|
||||
#
|
||||
# Note: If you want to use a "hydrophilic" chaperone (with h=0.0
|
||||
# instead of h=0.475), then replace the word "CHAP_INTERIOR_H0.475"
|
||||
# (at the end of "system.lt") with "CHAP_INTERIOR_H0"
|
||||
#
|
||||
# Because this process takes a long time (even with the help of the chaperone)
|
||||
# I save the data relatively infrequently.
|
||||
#
|
||||
# -------- REQUIREMENTS: ---------
|
||||
# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC")
|
||||
# http://lammps.sandia.gov/doc/Section_start.html#start_3
|
||||
# 2) It also may require additional features and bug fixes for LAMMPS.
|
||||
# be sure to download and copy the "additional_lammps_code" from
|
||||
# http://moltemplate.org (upper-left corner menu)
|
||||
# 3) Unpack it
|
||||
# 4) copy the .cpp and .h files to the src folding of your lammps installation.
|
||||
# 5) Compile LAMMPS.
|
||||
|
||||
-------------
|
||||
Instructions on how to build LAMMPS input files and
|
||||
run a short simulation are provided in other README files.
|
||||
|
||||
step 1)
|
||||
README_setup.sh
|
||||
|
||||
step2)
|
||||
README_run.sh
|
||||
|
|
@ -0,0 +1,31 @@
|
|||
# You would probably run lammps this way:
|
||||
#
|
||||
# lmp_ubuntu -i run.in.nvt
|
||||
|
||||
# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer
|
||||
# to the input scripts & data files you created earlier when you ran moltemplate
|
||||
# system.in.init, system.in.settings, system.data
|
||||
|
||||
|
||||
|
||||
|
||||
# -----------------------------------
|
||||
|
||||
|
||||
|
||||
LAMMPS_COMMAND="lmp_ubuntu"
|
||||
|
||||
# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps
|
||||
# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary.
|
||||
|
||||
# Run lammps using the following 3 commands:
|
||||
|
||||
"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL)
|
||||
"$LAMMPS_COMMAND" -i run.in.nvt # production run
|
||||
|
||||
# Alternately, if you have MPI installed, try something like this:
|
||||
|
||||
#NUMPROCS=4
|
||||
#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL)
|
||||
#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run
|
||||
|
||||
|
|
@ -0,0 +1,24 @@
|
|||
# Use these commands to generate the LAMMPS input script and data file
|
||||
# (and other auxilliary files):
|
||||
|
||||
|
||||
# Create LAMMPS input files this way:
|
||||
cd moltemplate_files
|
||||
|
||||
# run moltemplate
|
||||
|
||||
moltemplate.sh -overlay-dihdedrals system.lt
|
||||
|
||||
# This will generate various files with names ending in *.in* and *.data.
|
||||
# These files are the input files directly read by LAMMPS. Move them to
|
||||
# the parent directory (or wherever you plan to run the simulation).
|
||||
|
||||
mv -f system.in* system.data ../
|
||||
cp -r table*.dat ../
|
||||
|
||||
# Optional:
|
||||
# The "./output_ttree/" directory is full of temporary files generated by
|
||||
# moltemplate. They can be useful for debugging, but are usually thrown away.
|
||||
rm -rf output_ttree/
|
||||
|
||||
cd ../
|
||||
|
|
@ -0,0 +1,87 @@
|
|||
|
||||
------- To view a lammps trajectory in VMD --------
|
||||
|
||||
|
||||
1) Build a PSF file for use in viewing with VMD.
|
||||
|
||||
This step works with VMD 1.9 and topotools 1.2.
|
||||
(Older versions, like VMD 1.8.6, don't support this.)
|
||||
|
||||
|
||||
a) Start VMD
|
||||
b) Menu Extensions->Tk Console
|
||||
c) Enter:
|
||||
|
||||
(I assume that the the DATA file is called "system.data")
|
||||
|
||||
topo readlammpsdata system.data full
|
||||
animate write psf system.psf
|
||||
|
||||
2)
|
||||
|
||||
Later, to Load a trajectory in VMD:
|
||||
|
||||
Start VMD
|
||||
Select menu: File->New Molecule
|
||||
-Browse to select the PSF file you created above, and load it.
|
||||
(Don't close the window yet.)
|
||||
-Browse to select the trajectory file.
|
||||
If necessary, for "file type" select: "LAMMPS Trajectory"
|
||||
Load it.
|
||||
|
||||
---- A note on trajectory format: -----
|
||||
If the trajectory is a DUMP file, then make sure the it contains the
|
||||
information you need for pbctools (see below. I've been using this
|
||||
command in my LAMMPS scripts to create the trajectories:
|
||||
|
||||
dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
|
||||
|
||||
It's a good idea to use an atom_style which supports molecule-ID numbers
|
||||
so that you can assign a molecule-ID number to each atom. (I think this
|
||||
is needed to wrap atom coordinates without breaking molecules in half.)
|
||||
|
||||
Of course, you don't have to save your trajectories in DUMP format,
|
||||
(other formats like DCD work fine) I just mention dump files
|
||||
because these are the files I'm familiar with.
|
||||
|
||||
3) ----- Wrap the coordinates to the unit cell
|
||||
(without cutting the molecules in half)
|
||||
|
||||
a) Start VMD
|
||||
b) Load the trajectory in VMD (see above)
|
||||
c) Menu Extensions->Tk Console
|
||||
d) Try entering these commands:
|
||||
|
||||
pbc wrap -compound res -all
|
||||
pbc box
|
||||
|
||||
----- Optional ----
|
||||
Sometimes the solvent or membrane obscures the view of the solute.
|
||||
It can help to shift the location of the periodic boundary box
|
||||
To shift the box in the y direction (for example) do this:
|
||||
|
||||
pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
|
||||
pbc box -shiftcenterrel {0.0 0.15 0.0}
|
||||
|
||||
Distances are measured in units of box-length fractions, not Angstroms.
|
||||
|
||||
Alternately if you have a solute whose atoms are all of type 1,
|
||||
then you can also try this to center the box around it:
|
||||
|
||||
pbc wrap -sel type=1 -all -centersel type=2 -center com
|
||||
|
||||
4)
|
||||
You should check if your periodic boundary conditions are too small.
|
||||
To do that:
|
||||
select Graphics->Representations menu option
|
||||
click on the "Periodic" tab, and
|
||||
click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
|
||||
|
||||
5) Optional: If you like, change the atom types in the PSF file so
|
||||
that VMD recognizes the atom types, use something like:
|
||||
|
||||
sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
|
||||
sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
|
||||
sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
|
||||
|
||||
(If you do this, it might effect step 2 above.)
|
||||
|
|
@ -0,0 +1,86 @@
|
|||
PSF
|
||||
|
||||
1 !NTITLE
|
||||
REMARKS VMD generated structure x-plor psf file
|
||||
|
||||
28 !NATOM
|
||||
1 1 2 2 0.000000 1.0000 0
|
||||
2 1 1 1 0.000000 1.0000 0
|
||||
3 1 2 2 0.000000 1.0000 0
|
||||
4 1 1 1 0.000000 1.0000 0
|
||||
5 1 2 2 0.000000 1.0000 0
|
||||
6 1 1 1 0.000000 1.0000 0
|
||||
7 1 3 3 0.000000 1.0000 0
|
||||
8 1 3 3 0.000000 1.0000 0
|
||||
9 1 1 1 0.000000 1.0000 0
|
||||
10 1 2 2 0.000000 1.0000 0
|
||||
11 1 1 1 0.000000 1.0000 0
|
||||
12 1 2 2 0.000000 1.0000 0
|
||||
13 1 1 1 0.000000 1.0000 0
|
||||
14 1 2 2 0.000000 1.0000 0
|
||||
15 1 3 3 0.000000 1.0000 0
|
||||
16 1 3 3 0.000000 1.0000 0
|
||||
17 1 3 3 0.000000 1.0000 0
|
||||
18 1 1 1 0.000000 1.0000 0
|
||||
19 1 1 1 0.000000 1.0000 0
|
||||
20 1 2 2 0.000000 1.0000 0
|
||||
21 1 2 2 0.000000 1.0000 0
|
||||
22 1 1 1 0.000000 1.0000 0
|
||||
23 1 1 1 0.000000 1.0000 0
|
||||
24 1 2 2 0.000000 1.0000 0
|
||||
25 1 2 2 0.000000 1.0000 0
|
||||
26 1 1 1 0.000000 1.0000 0
|
||||
27 1 2 2 0.000000 1.0000 0
|
||||
28 2 4 4 0.000000 100.0000 0
|
||||
|
||||
26 !NBOND: bonds
|
||||
1 2 2 3 3 4 4 5
|
||||
5 6 6 7 7 8 8 9
|
||||
9 10 10 11 11 12 12 13
|
||||
13 14 14 15 15 16 16 17
|
||||
17 18 18 19 19 20 20 21
|
||||
21 22 22 23 23 24 24 25
|
||||
25 26 26 27
|
||||
|
||||
25 !NTHETA: angles
|
||||
13 14 15 7 8 9 6 7 8
|
||||
16 17 18 15 16 17 2 3 4
|
||||
4 5 6 9 10 11 11 12 13
|
||||
14 15 16 1 2 3 3 4 5
|
||||
10 11 12 12 13 14 25 26 27
|
||||
5 6 7 8 9 10 17 18 19
|
||||
18 19 20 22 23 24 21 22 23
|
||||
19 20 21 20 21 22 23 24 25
|
||||
24 25 26
|
||||
|
||||
19 !NPHI: dihedrals
|
||||
1 2 3 4 2 3 4 5
|
||||
3 4 5 6 4 5 6 7
|
||||
8 9 10 11 9 10 11 12
|
||||
10 11 12 13 11 12 13 14
|
||||
12 13 14 15 15 16 17 18
|
||||
16 17 18 19 17 18 19 20
|
||||
18 19 20 21 19 20 21 22
|
||||
20 21 22 23 21 22 23 24
|
||||
22 23 24 25 23 24 25 26
|
||||
24 25 26 27
|
||||
|
||||
0 !NIMPHI: impropers
|
||||
|
||||
|
||||
0 !NDON: donors
|
||||
|
||||
|
||||
0 !NACC: acceptors
|
||||
|
||||
|
||||
0 !NNB
|
||||
|
||||
0 0 0 0 0 0 0 0
|
||||
0 0 0 0 0 0 0 0
|
||||
0 0 0 0 0 0 0 0
|
||||
0 0 0 0
|
||||
|
||||
1 0 !NGRP
|
||||
0 0 0
|
||||
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 15 KiB |
Binary file not shown.
|
After Width: | Height: | Size: 17 KiB |
|
|
@ -0,0 +1,216 @@
|
|||
# This file defines the "frustrated" coarse-grained protein model used in:
|
||||
# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
|
||||
# (http://www.pnas.org/content/101/36/13192)
|
||||
|
||||
|
||||
1beadFrustrated {
|
||||
|
||||
# There are 3 atom types (referred to above as B, L, and N)
|
||||
# Define their masses:
|
||||
|
||||
write_once("Data Masses") {
|
||||
@atom:B 1.0
|
||||
@atom:L 1.0
|
||||
@atom:N 1.0
|
||||
}
|
||||
|
||||
# AtomID MoleculeID AtomType Charge X Y Z
|
||||
|
||||
write('Data Atoms') {
|
||||
$atom:a1 $mol @atom:L 0.0 -0.92636654 -1.8409904 -2.1482679
|
||||
$atom:a2 $mol @atom:B 0.0 -0.57313354 -1.0670787 -1.6182341
|
||||
$atom:a3 $mol @atom:L 0.0 -0.85707399 -1.2358703 -0.69350966
|
||||
$atom:a4 $mol @atom:B 0.0 -0.44231274 -0.4584993 -0.23418709
|
||||
$atom:a5 $mol @atom:L 0.0 -0.75081182 -0.62868078 0.69786737
|
||||
$atom:a6 $mol @atom:B 0.0 -0.36201977 0.11619615 1.2249098
|
||||
$atom:a7 $mol @atom:N 0.0 -0.63708237 -0.15973084 2.1723919
|
||||
$atom:a8 $mol @atom:N 0.0 0.20516047 0.10417157 2.624901
|
||||
$atom:a9 $mol @atom:B 0.0 0.57223743 0.44728103 1.7695617
|
||||
$atom:a10 $mol @atom:L 0.0 0.77646279 -0.40630393 1.3168043
|
||||
$atom:a11 $mol @atom:B 0.0 0.45475664 -0.2077937 0.40045721
|
||||
$atom:a12 $mol @atom:L 0.0 0.72712495 -1.0397637 -0.087614951
|
||||
$atom:a13 $mol @atom:B 0.0 0.36971183 -0.85840501 -0.9933019
|
||||
$atom:a14 $mol @atom:L 0.0 0.74784336 -1.5700415 -1.5859217
|
||||
$atom:a15 $mol @atom:N 0.0 0.43423905 -1.2758917 -2.4853429
|
||||
$atom:a16 $mol @atom:N 0.0 0.70583191 -0.30726921 -2.4987711
|
||||
$atom:a17 $mol @atom:N 0.0 -0.091688915 0.23323014 -2.2051358
|
||||
$atom:a18 $mol @atom:B 0.0 -0.34243283 -0.035822049 -1.2644719
|
||||
$atom:a19 $mol @atom:B 0.0 0.41961247 0.18475451 -0.65971014
|
||||
$atom:a20 $mol @atom:L 0.0 0.51968465 1.1546791 -0.77877053
|
||||
$atom:a21 $mol @atom:L 0.0 -0.40827985 1.2765273 -0.52550748
|
||||
$atom:a22 $mol @atom:B 0.0 -0.368141 0.58090904 0.19152224
|
||||
$atom:a23 $mol @atom:B 0.0 0.40327249 0.86101769 0.7336255
|
||||
$atom:a24 $mol @atom:L 0.0 0.22707289 1.8326235 0.89673346
|
||||
$atom:a25 $mol @atom:L 0.0 -0.66500182 1.7285809 1.2783166
|
||||
$atom:a26 $mol @atom:B 0.0 -0.39205603 1.0475436 1.9328097
|
||||
$atom:a27 $mol @atom:L 0.0 0.25339027 1.5246265 2.5388463
|
||||
}
|
||||
|
||||
# bond-ID bond-Type atom-ID atom-ID
|
||||
|
||||
write('Data Bonds') {
|
||||
$bond:b1 @bond:backbone $atom:a1 $atom:a2
|
||||
$bond:b2 @bond:backbone $atom:a2 $atom:a3
|
||||
$bond:b3 @bond:backbone $atom:a3 $atom:a4
|
||||
$bond:b4 @bond:backbone $atom:a4 $atom:a5
|
||||
$bond:b5 @bond:backbone $atom:a5 $atom:a6
|
||||
$bond:b6 @bond:backbone $atom:a6 $atom:a7
|
||||
$bond:b7 @bond:backbone $atom:a7 $atom:a8
|
||||
$bond:b8 @bond:backbone $atom:a8 $atom:a9
|
||||
$bond:b9 @bond:backbone $atom:a9 $atom:a10
|
||||
$bond:b10 @bond:backbone $atom:a10 $atom:a11
|
||||
$bond:b11 @bond:backbone $atom:a11 $atom:a12
|
||||
$bond:b12 @bond:backbone $atom:a12 $atom:a13
|
||||
$bond:b13 @bond:backbone $atom:a13 $atom:a14
|
||||
$bond:b14 @bond:backbone $atom:a14 $atom:a15
|
||||
$bond:b15 @bond:backbone $atom:a15 $atom:a16
|
||||
$bond:b16 @bond:backbone $atom:a16 $atom:a17
|
||||
$bond:b17 @bond:backbone $atom:a17 $atom:a18
|
||||
$bond:b18 @bond:backbone $atom:a18 $atom:a19
|
||||
$bond:b19 @bond:backbone $atom:a19 $atom:a20
|
||||
$bond:b20 @bond:backbone $atom:a20 $atom:a21
|
||||
$bond:b21 @bond:backbone $atom:a21 $atom:a22
|
||||
$bond:b22 @bond:backbone $atom:a22 $atom:a23
|
||||
$bond:b23 @bond:backbone $atom:a23 $atom:a24
|
||||
$bond:b24 @bond:backbone $atom:a24 $atom:a25
|
||||
$bond:b25 @bond:backbone $atom:a25 $atom:a26
|
||||
$bond:b26 @bond:backbone $atom:a26 $atom:a27
|
||||
}
|
||||
|
||||
# (3-body) Angles are specified below
|
||||
|
||||
# (4-body) Dihedrals must be defined explicitly for every quartet of atoms.
|
||||
# (These interactions are not determined by atom type.)
|
||||
|
||||
# dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID
|
||||
|
||||
write('Data Dihedrals') {
|
||||
|
||||
$dihedral:d1 @dihedral:beta $atom:a1 $atom:a2 $atom:a3 $atom:a4
|
||||
$dihedral:d2 @dihedral:beta $atom:a2 $atom:a3 $atom:a4 $atom:a5
|
||||
$dihedral:d3 @dihedral:beta $atom:a3 $atom:a4 $atom:a5 $atom:a6
|
||||
$dihedral:d4 @dihedral:beta $atom:a4 $atom:a5 $atom:a6 $atom:a7
|
||||
|
||||
# Dihedral angle forces in the turn regions were switched off
|
||||
# (in this model) so just I comment them out (and \ the variable names).
|
||||
# \$dihedral:d5 \@dihedral:turn $atom:a5 $atom:a6 $atom:a7 $atom:a8
|
||||
# \$dihedral:d6 \@dihedral:turn $atom:a6 $atom:a7 $atom:a8 $atom:a9
|
||||
# \$dihedral:d7 \@dihedral:turn $atom:a7 $atom:a8 $atom:a9 $atom:a10
|
||||
|
||||
$dihedral:d8 @dihedral:beta $atom:a8 $atom:a9 $atom:a10 $atom:a11
|
||||
$dihedral:d9 @dihedral:beta $atom:a9 $atom:a10 $atom:a11 $atom:a12
|
||||
$dihedral:d10 @dihedral:beta $atom:a10 $atom:a11 $atom:a12 $atom:a13
|
||||
$dihedral:d11 @dihedral:beta $atom:a11 $atom:a12 $atom:a13 $atom:a14
|
||||
$dihedral:d12 @dihedral:beta $atom:a12 $atom:a13 $atom:a14 $atom:a15
|
||||
|
||||
# Dihedral angle forces in the turn regions were switched off
|
||||
# (in this model) so just I comment them out (and \ the variable names).
|
||||
# \$dihedral:d13 \@dihedral:turn $atom:a13 $atom:a14 $atom:a15 $atom:a16
|
||||
# \$dihedral:d14 \@dihedral:turn $atom:a14 $atom:a15 $atom:a16 $atom:a17
|
||||
|
||||
$dihedral:d15 @dihedral:alpha $atom:a15 $atom:a16 $atom:a17 $atom:a18
|
||||
$dihedral:d16 @dihedral:alpha $atom:a16 $atom:a17 $atom:a18 $atom:a19
|
||||
$dihedral:d17 @dihedral:alpha $atom:a17 $atom:a18 $atom:a19 $atom:a20
|
||||
$dihedral:d18 @dihedral:alpha $atom:a18 $atom:a19 $atom:a20 $atom:a21
|
||||
$dihedral:d19 @dihedral:alpha $atom:a19 $atom:a20 $atom:a21 $atom:a22
|
||||
$dihedral:d20 @dihedral:alpha $atom:a20 $atom:a21 $atom:a22 $atom:a23
|
||||
$dihedral:d21 @dihedral:alpha $atom:a21 $atom:a22 $atom:a23 $atom:a24
|
||||
$dihedral:d22 @dihedral:alpha $atom:a22 $atom:a23 $atom:a24 $atom:a25
|
||||
$dihedral:d23 @dihedral:alpha $atom:a23 $atom:a24 $atom:a25 $atom:a26
|
||||
$dihedral:d24 @dihedral:alpha $atom:a24 $atom:a25 $atom:a26 $atom:a27
|
||||
}
|
||||
|
||||
# All consecutively bonded triplets of atoms same 3-body bond-angle
|
||||
# interaction parameters. Of coarse, we could specify them all explicitly
|
||||
# (as we did for the dihedrals above), but I wanted to show how to specify
|
||||
# angles by atom type instead. (You can do this for dihedrals & impropers
|
||||
# also.)
|
||||
|
||||
# angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type
|
||||
|
||||
write_once('Data Angles By Type') {
|
||||
@angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:*
|
||||
}
|
||||
|
||||
# (The "*" is a wildcard character. I use "*" to denote any atom-type or
|
||||
# bond-type which is defined within the current namespace: 1beadFrustrated)
|
||||
|
||||
|
||||
# 2-body (non-bonded) interactions:
|
||||
#
|
||||
# Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6)
|
||||
#
|
||||
# i j pairstylename eps sig K L
|
||||
#
|
||||
write_once("In Settings") {
|
||||
pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1
|
||||
pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0
|
||||
pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0
|
||||
pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1
|
||||
pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0
|
||||
pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0
|
||||
}
|
||||
|
||||
|
||||
# 2-body (bonded) interactions:
|
||||
#
|
||||
# Ubond(r) = (k/2)*(r-0)^2
|
||||
#
|
||||
# The corresponding command is:
|
||||
#
|
||||
# bond-Type bondstylename k r0
|
||||
|
||||
write_once("In Settings") {
|
||||
bond_coeff @bond:backbone harmonic 100.0 1.0
|
||||
}
|
||||
|
||||
# 3-body interactions in this example are listed by atomType and bondType
|
||||
# The atomIDs involved are determined automatically. The forumula used is:
|
||||
#
|
||||
# Uangle(theta) = (k/2)*(theta-theta0)^2
|
||||
# (k in kcal/mol/rad^2, theta0 in degrees)
|
||||
#
|
||||
# angle-Type anglestylename k theta0
|
||||
|
||||
write_once("In Settings") {
|
||||
angle_coeff @angle:backbone harmonic 13.3333333333 105.0
|
||||
}
|
||||
|
||||
|
||||
# We use tabular dihedral potentials to implement the dihedral forces.
|
||||
# (Actually there is a way to use Fourier series, using multiple charmm
|
||||
# style dihedral interactions, but it's slower and messier.)
|
||||
|
||||
write_once("In Settings") {
|
||||
# style file keyword
|
||||
dihedral_coeff @dihedral:alpha table table_dihedral_frustrated.dat FRUSTRATED_ALPHA
|
||||
dihedral_coeff @dihedral:beta table table_dihedral_frustrated.dat FRUSTRATED_BETA
|
||||
# No need to specify dihedral interactions in the turn regions. (none exist)
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
# Optional: define the atoms in the "proteins" group
|
||||
group proteins type @atom:B
|
||||
group proteins type @atom:L
|
||||
group proteins type @atom:N
|
||||
}
|
||||
|
||||
# LAMMPS has many available force field styles (and atom styles).
|
||||
# Here, we pick the ones which work well for this molecular model:
|
||||
|
||||
write_once("In Init") {
|
||||
# --- Default options for the "1BeadFrustrated" protein model ---
|
||||
# --- (These can be overridden later.) ---
|
||||
units lj
|
||||
atom_style full
|
||||
bond_style hybrid harmonic
|
||||
angle_style hybrid harmonic
|
||||
dihedral_style hybrid table spline 360
|
||||
pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0
|
||||
pair_modify mix arithmetic
|
||||
special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions)
|
||||
}
|
||||
|
||||
} # 1beadFrustrated
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,85 @@
|
|||
import "1beadFrustrated.lt"
|
||||
|
||||
|
||||
# Alternate starting conformation (same molecule):
|
||||
|
||||
|
||||
1beadMisfolded inherits 1beadFrustrated {
|
||||
|
||||
# This molecule "inherits" all of its features from "1beadFrustrated".
|
||||
# Here we override the atomic positions with new coordinates:
|
||||
|
||||
# AtomID MoleculeID AtomType Charge X Y Z
|
||||
|
||||
write("Data Atoms") {
|
||||
$atom:a1 $mol @atom:L 0.0 -0.69801399 -0.22114168 -1.9464876
|
||||
$atom:a2 $mol @atom:B 0.0 -0.40921658 -0.027063664 -1.0033251
|
||||
$atom:a3 $mol @atom:L 0.0 0.10259348 0.80836418 -1.0737085
|
||||
$atom:a4 $mol @atom:B 0.0 0.25857916 1.0054984 -0.11621451
|
||||
$atom:a5 $mol @atom:L 0.0 0.8258629 1.8325549 -0.18529135
|
||||
$atom:a6 $mol @atom:B 0.0 0.91366257 2.1950317 0.74175977
|
||||
$atom:a7 $mol @atom:N 0.0 1.4399539 1.554238 1.2994409
|
||||
$atom:a8 $mol @atom:N 0.0 0.73372573 1.0161012 1.7397275
|
||||
$atom:a9 $mol @atom:B 0.0 0.26608782 0.65302497 0.94353938
|
||||
$atom:a10 $mol @atom:L 0.0 0.97442305 0.13574211 0.50586398
|
||||
$atom:a11 $mol @atom:B 0.0 0.35889617 -0.18247555 -0.1764186
|
||||
$atom:a12 $mol @atom:L 0.0 0.87151735 -0.77260824 -0.75240916
|
||||
$atom:a13 $mol @atom:B 0.0 0.047726486 -1.0530682 -1.1902704
|
||||
$atom:a14 $mol @atom:L 0.0 0.34530697 -1.7476773 -1.8393331
|
||||
$atom:a15 $mol @atom:N 0.0 0.65865186 -2.45948 -1.2167056
|
||||
$atom:a16 $mol @atom:N 0.0 -0.16534524 -2.6219442 -0.67112167
|
||||
$atom:a17 $mol @atom:N 0.0 -0.010590421 -2.2445242 0.24748633
|
||||
$atom:a18 $mol @atom:B 0.0 0.18135771 -1.2564919 0.1767523
|
||||
$atom:a19 $mol @atom:B 0.0 -0.57472665 -0.82852797 -0.27027791
|
||||
$atom:a20 $mol @atom:L 0.0 -1.3967448 -1.0516787 0.24247346
|
||||
$atom:a21 $mol @atom:L 0.0 -1.003428 -0.85642681 1.1107555
|
||||
$atom:a22 $mol @atom:B 0.0 -0.25156735 -0.3182346 0.74262946
|
||||
$atom:a23 $mol @atom:B 0.0 -0.61751956 0.30115562 0.070426493
|
||||
$atom:a24 $mol @atom:L 0.0 -1.3347934 0.83310182 0.52625934
|
||||
$atom:a25 $mol @atom:L 0.0 -0.83315257 1.270904 1.2564086
|
||||
$atom:a26 $mol @atom:B 0.0 -0.10469759 1.6988523 0.72597181
|
||||
$atom:a27 $mol @atom:L 0.0 -0.57854905 2.3367737 0.11206868
|
||||
}
|
||||
|
||||
} # 1beadMisfolded
|
||||
|
||||
|
||||
1beadUnfolded inherits 1beadFrustrated {
|
||||
|
||||
# This molecule "inherits" all of its features from "1beadFrustrated"
|
||||
# Here we override the atomic positions with new coordinates:
|
||||
|
||||
# AtomID MoleculeID AtomType Charge X Y Z
|
||||
|
||||
write('Data Atoms') {
|
||||
$atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0
|
||||
$atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8
|
||||
$atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8
|
||||
$atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0
|
||||
$atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0
|
||||
$atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8
|
||||
$atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8
|
||||
$atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0
|
||||
$atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0
|
||||
$atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8
|
||||
$atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8
|
||||
$atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0
|
||||
$atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0
|
||||
$atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8
|
||||
$atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8
|
||||
$atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2
|
||||
$atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2
|
||||
$atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6
|
||||
$atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6
|
||||
$atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2
|
||||
$atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2
|
||||
$atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6
|
||||
$atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6
|
||||
$atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2
|
||||
$atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2
|
||||
$atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6
|
||||
$atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6
|
||||
}
|
||||
|
||||
} # 1beadUnfolded
|
||||
|
||||
|
|
@ -0,0 +1,41 @@
|
|||
# Here we define a trivial molecule containing only one particle.
|
||||
|
||||
Chaperonin {
|
||||
|
||||
# atomID molID atomType charge x y z
|
||||
|
||||
write("Data Atoms") {
|
||||
$atom:C $mol @atom:C 0.0 0.0 0.0 0.0
|
||||
}
|
||||
|
||||
write_once("Data Masses") {
|
||||
@atom:C 100.0
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
# If for some reason there are multiple chaperones present,
|
||||
# I assume that they interact repulsively (hence, L=0)
|
||||
# i j epsilon sigma K L
|
||||
|
||||
pair_coeff @atom:C @atom:C lj/charmm/coul/charmm/inter 1.0 6.0 1 0
|
||||
|
||||
# Optional: define the atoms in the "chaperonins" group:
|
||||
# (Defining a group for the chaperone makes it easy to immobilize it later.)
|
||||
|
||||
group chaperonins type @atom:C
|
||||
}
|
||||
|
||||
|
||||
# Specify which pair_styles, and atom styles work well with
|
||||
# this model. (Again this can be overridden later.)
|
||||
|
||||
write_once("In Init") {
|
||||
units lj
|
||||
atom_style full
|
||||
pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 11.0 12.0
|
||||
}
|
||||
|
||||
} # Chaperonin
|
||||
|
||||
# We have not specified how this particle interacts with other particles
|
||||
# besides itself. Later on you must do this.
|
||||
|
|
@ -0,0 +1,87 @@
|
|||
#!/usr/bin/env python
|
||||
|
||||
# Calculate a table of pairwise energies and forces between atoms in the
|
||||
# protein and a chaperone provided in the supplemental materials section of:
|
||||
# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
|
||||
# This is stored in a tabulated force field with a singularity at a distance R.
|
||||
#
|
||||
# To calculate the table for interaction between
|
||||
# ...the chaperone and a hydrophobic bead (2004 PNAS paper), use this table:
|
||||
# ./calc_chaperone_table.py 1.0 1.0 6.0 0.475 0.0 5.9 1181
|
||||
# ...the chaperone and a hydrophilic bead (2004 PNAS paper), use this table:
|
||||
# ./calc_chaperone_table.py 1.0 1.0 6.0 0.0 0.0 5.9 1181
|
||||
# ...the chaperone and a hydrophobic bead (2006 JMB paper), use this table:
|
||||
# ./calc_chaperone_table.py 1.0 1.0 3.0 0.60 3.1 8.0 981 True
|
||||
# ...the chaperone and a hydrophilic bead (2006 JMB paper), use this table:
|
||||
# ./calc_chaperone_table.py 1.0 1.0 3.0 0.0 3.1 8.0 981 True
|
||||
|
||||
from math import *
|
||||
import sys
|
||||
|
||||
def U(r, eps, sigma, R, h):
|
||||
#print('r='+str(r)+' eps='+str(eps)+' s='+str(sigma)+' R='+str(R)+' h='+str(h))
|
||||
# Formula is undefined at r=0, but you can take the limit:
|
||||
if r <= 0:
|
||||
return 4.0*pi*R*R*4.0*eps*(pow((sigma/R), 12.0)
|
||||
- h*pow((sigma/R), 6.0))
|
||||
xp = sigma/(r+R)
|
||||
xm = sigma/(r-R)
|
||||
term10 = pow(xm, 10.0) - pow(xp, 10.0)
|
||||
term4 = pow(xm, 4.0) - pow(xp, 4.0)
|
||||
return 4.0*pi*eps*(R/r) * (0.2*term10 - 0.5*h*term4)
|
||||
|
||||
def F(r, eps, sigma, R, h):
|
||||
# Formula is undefined at r=0, but you can take the limit:
|
||||
if r <= 0:
|
||||
return 0.0
|
||||
product_term_a = U(r, eps, sigma, R, h) / r
|
||||
ixp = (r+R)/sigma
|
||||
ixm = (r-R)/sigma
|
||||
dix_dr = 1.0/sigma
|
||||
term10 = (10.0/sigma)*(pow(ixm, -11.0) - pow(ixp, -11.0))
|
||||
term4 = (4.0/sigma)*(pow(ixm, -5.0) - pow(ixp, -5.0))
|
||||
product_term_b = 4.0*eps*pi*(R/r) * (0.2*term10 - 0.5*h*term4)
|
||||
return product_term_a + product_term_b
|
||||
|
||||
|
||||
class InputError(Exception):
|
||||
""" A generic exception object containing a string for error reporting.
|
||||
|
||||
"""
|
||||
def __init__(self, err_msg):
|
||||
self.err_msg = err_msg
|
||||
def __str__(self):
|
||||
return self.err_msg
|
||||
def __repr__(self):
|
||||
return str(self)
|
||||
|
||||
if len(sys.argv) < 8:
|
||||
sys.stderr.write("Error: expected 7 arguments:\n"
|
||||
"\n"
|
||||
"Usage: "+sys.argv[0]+" epsilon sigma R h rmin rmax N\n\n")
|
||||
sys.exit(-1)
|
||||
|
||||
epsilon = float(sys.argv[1])
|
||||
sigma = float(sys.argv[2])
|
||||
R = float(sys.argv[3])
|
||||
h = float(sys.argv[4])
|
||||
rmin = float(sys.argv[5])
|
||||
rmax = float(sys.argv[6])
|
||||
N = int(sys.argv[7])
|
||||
|
||||
subtract_Urcut = False
|
||||
if len(sys.argv) == 9:
|
||||
subtract_Urcut = True
|
||||
rcut = rmax
|
||||
|
||||
for i in range(0,N):
|
||||
r = rmin + i*(rmax-rmin)/(N-1)
|
||||
U_r = U(r, epsilon, sigma, R, h)
|
||||
F_r = F(r, epsilon, sigma, R, h)
|
||||
if subtract_Urcut:
|
||||
U_r -= U(rcut, epsilon, sigma, R, h)
|
||||
if (r >= rcut) or (i==N-1):
|
||||
U_r = 0.0
|
||||
F_r = 0.0
|
||||
print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))
|
||||
|
||||
|
|
@ -0,0 +1,67 @@
|
|||
#!/usr/bin/env python
|
||||
|
||||
# Calculate a table of dihedral angle interactions used in the alpha-helix
|
||||
# and beta-sheet regions of the frustrated protein model described in
|
||||
# provided in figure 8 of the supplemental materials section of:
|
||||
# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
|
||||
# Note that the "A" and "B" parameters were incorrectly reported to be
|
||||
# 5.4*epsilon and 6.0*epsilon. The values used were 5.6 and 6.0 epsilon.
|
||||
# The phiA and phiB values were 57.29577951308232 degrees (1 rad)
|
||||
# and 180 degrees, respectively. Both expA and expB were 6.0.
|
||||
#
|
||||
# To generate the table used for the alpha-helix (1 degree resolution) use this:
|
||||
# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360
|
||||
# To generate the table used for the beta-sheets (1 degree resolution) use this:
|
||||
# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360
|
||||
#
|
||||
# (If you're curious as to why I set the location of the minima at phi_alpha
|
||||
# to 1.0 radians (57.2957795 degrees), there was no particularly good reason.
|
||||
# I think the correct value turns out to be something closer to 50 degrees.)
|
||||
|
||||
|
||||
from math import *
|
||||
import sys
|
||||
|
||||
|
||||
# The previous version included the repulsive core term
|
||||
def U(phi, A, phiA, expA, B, phiB, expB, use_radians=False):
|
||||
conv_units = pi/180.0
|
||||
if use_radians:
|
||||
conv_units = 1.0
|
||||
termA = pow(cos(0.5*(phi-phiA)*conv_units), expA)
|
||||
termB = pow(cos(0.5*(phi-phiB)*conv_units), expB)
|
||||
return -A*termA - B*termB
|
||||
|
||||
# The previous version included the repulsive core term
|
||||
def F(phi, A, phiA, expA, B, phiB, expB, use_radians=False):
|
||||
conv_units = pi/180.0
|
||||
if use_radians:
|
||||
conv_units = 1.0
|
||||
termA = (0.5*sin(0.5*(phi-phiA)*conv_units) *
|
||||
expA * pow(cos(0.5*(phi-phiA)*conv_units), expA-1.0))
|
||||
termB = (0.5*sin(0.5*(phi-phiB)*conv_units) *
|
||||
expB * pow(cos(0.5*(phi-phiB)*conv_units), expB-1.0))
|
||||
return -conv_units*(A*termA + B*termB)
|
||||
|
||||
if len(sys.argv) != 10:
|
||||
sys.stderr.write("Error: expected 9 arguments:\n"
|
||||
"\n"
|
||||
"Usage: "+sys.argv[0]+" A phiA expA B phiB expB phiMin phiMax N\n\n")
|
||||
sys.exit(-1)
|
||||
|
||||
A = float(sys.argv[1])
|
||||
phiA = float(sys.argv[2])
|
||||
expA = float(sys.argv[3])
|
||||
B = float(sys.argv[4])
|
||||
phiB = float(sys.argv[5])
|
||||
expB = float(sys.argv[6])
|
||||
phi_min = float(sys.argv[7])
|
||||
phi_max = float(sys.argv[8])
|
||||
N = int(sys.argv[9])
|
||||
|
||||
for i in range(0,N):
|
||||
phi = phi_min + i*(phi_max - phi_min)/(N-1)
|
||||
U_phi = U(phi, A, phiA, expA, B, phiB, expB, use_radians=False)
|
||||
F_phi = F(phi, A, phiA, expA, B, phiB, expB, use_radians=False)
|
||||
print(str(i+1)+' '+str(phi)+' '+str(U_phi)+' '+str(F_phi))
|
||||
|
||||
|
|
@ -0,0 +1,45 @@
|
|||
write_once("Data Boundary") {
|
||||
0.0 20.0 xlo xhi
|
||||
0.0 20.0 ylo yhi
|
||||
0.0 20.0 zlo zhi
|
||||
}
|
||||
|
||||
|
||||
import "1beadFrustrated_variants.lt"
|
||||
import "chaperonin.lt"
|
||||
|
||||
|
||||
protein = new 1beadMisfolded # (frustrated protein, misfolded conformation)
|
||||
chaperinin = new Chaperonin # (hollow chaperonin cavity. usually immobile)
|
||||
|
||||
|
||||
|
||||
# ---- Now define interactions between the atoms in the protein ----
|
||||
# ---- (named "B", "L", "N") and the atom which represents the ----
|
||||
# ---- chaperone ("C"). These interactions are tabulated. ----
|
||||
|
||||
write_once("In Settings") {
|
||||
pair_coeff @atom:Chaperonin/C @atom:1beadFrustrated/B table table_chaperonin_h=0.475.dat CH_H0.475
|
||||
pair_coeff @atom:Chaperonin/C @atom:1beadFrustrated/L table table_chaperonin_h=0.dat CH_H0
|
||||
pair_coeff @atom:Chaperonin/C @atom:1beadFrustrated/N table table_chaperonin_h=0.dat CH_H0
|
||||
}
|
||||
|
||||
# Note: If you want to use a "hydrophilic" chaperone (with h=0, not h=0.475)
|
||||
# then replace "table_chaperonin_h=0_475.dat CH_H0.475"
|
||||
# with "table_chaperonin_h=0.dat CH_H0"
|
||||
|
||||
# LAMMPS has many available force field styles (and atom styles). Here we
|
||||
# select the ones which work well for the full combine system. (This should
|
||||
# override any settings made in "1beadFrustrated.lt" or "chaperonin.lt")
|
||||
|
||||
|
||||
write_once("In Init") {
|
||||
units lj
|
||||
atom_style full
|
||||
bond_style hybrid harmonic
|
||||
angle_style hybrid harmonic
|
||||
dihedral_style hybrid table spline 360
|
||||
pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 table spline 1181
|
||||
pair_modify mix arithmetic
|
||||
special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions)
|
||||
}
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,735 @@
|
|||
# Table of the potential and its negative derivative for frustrated alpha helix
|
||||
# (Note: Derivatives are in units of energy/radians, not energy/degrees.)
|
||||
# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360
|
||||
|
||||
FRUSTRATED_ALPHA
|
||||
N 360 DEGREES
|
||||
|
||||
1 0.0 -2.74081145103 0.0783990792662
|
||||
2 1.0 -2.81950869101 0.0789852583442
|
||||
3 2.0 -2.89876136749 0.0795096391909
|
||||
4 3.0 -2.97850675562 0.0799703813963
|
||||
5 4.0 -3.05868032959 0.0803657243943
|
||||
6 5.0 -3.13921584545 0.0806939935737
|
||||
7 6.0 -3.22004543014 0.0809536062381
|
||||
8 7.0 -3.30109967628 0.0811430773977
|
||||
9 8.0 -3.38230774267 0.0812610253741
|
||||
10 9.0 -3.46359746038 0.0813061772009
|
||||
11 10.0 -3.54489544401 0.0812773738039
|
||||
12 11.0 -3.62612720812 0.0811735749433
|
||||
13 12.0 -3.70721728841 0.0809938639029
|
||||
14 13.0 -3.78808936748 0.080737451911
|
||||
15 14.0 -3.86866640485 0.0804036822781
|
||||
16 15.0 -3.94887077101 0.0799920342374
|
||||
17 16.0 -4.02862438516 0.0795021264757
|
||||
18 17.0 -4.10784885622 0.0789337203415
|
||||
19 18.0 -4.18646562704 0.0782867227197
|
||||
20 19.0 -4.26439612115 0.0775611885609
|
||||
21 20.0 -4.34156189202 0.0767573230567
|
||||
22 21.0 -4.41788477419 0.0758754834523
|
||||
23 22.0 -4.49328703609 0.0749161804868
|
||||
24 23.0 -4.56769153408 0.0738800794563
|
||||
25 24.0 -4.64102186743 0.0727680008923
|
||||
26 25.0 -4.71320253365 0.0715809208518
|
||||
27 26.0 -4.78415908407 0.0703199708131
|
||||
28 27.0 -4.85381827903 0.0689864371778
|
||||
29 28.0 -4.92210824234 0.067581760373
|
||||
30 29.0 -4.98895861476 0.0661075335571
|
||||
31 30.0 -5.05430070586 0.0645655009259
|
||||
32 31.0 -5.11806764409 0.0629575556235
|
||||
33 32.0 -5.18019452449 0.061285737258
|
||||
34 33.0 -5.24061855376 0.0595522290273
|
||||
35 34.0 -5.29927919225 0.0577593544584
|
||||
36 35.0 -5.3561182925 0.0559095737673
|
||||
37 36.0 -5.41108023395 0.0540054798439
|
||||
38 37.0 -5.46411205346 0.0520497938726
|
||||
39 38.0 -5.51516357127 0.0500453605949
|
||||
40 39.0 -5.56418751203 0.0479951432253
|
||||
41 40.0 -5.61113962059 0.0459022180302
|
||||
42 41.0 -5.65597877221 0.0437697685824
|
||||
43 42.0 -5.69866707689 0.0416010797029
|
||||
44 43.0 -5.7391699774 0.0393995311046
|
||||
45 44.0 -5.77745634094 0.0371685907508
|
||||
46 45.0 -5.81349854393 0.034911807945
|
||||
47 46.0 -5.84727254977 0.0326328061676
|
||||
48 47.0 -5.87875797937 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
|
||||
|
|
@ -0,0 +1,25 @@
|
|||
# -- Init section --
|
||||
|
||||
include system.in.init
|
||||
|
||||
# -- Atom definition section --
|
||||
|
||||
read_data system.data
|
||||
|
||||
# -- Settings Section --
|
||||
|
||||
include system.in.settings
|
||||
|
||||
# Optional: Make sure the pairwise energies look reasonable:
|
||||
pair_write 1 4 1001 r 0.00000000001 5.05 test_chap-B.dat C-B 0 0
|
||||
pair_write 2 4 1001 r 0.00000000001 5.05 test_chap-L.dat C-L 0 0
|
||||
pair_write 3 4 1001 r 0.00000000001 5.05 test_chap-N.dat C-N 0 0
|
||||
|
||||
|
||||
# -- Run section --
|
||||
|
||||
dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz
|
||||
|
||||
minimize 1.0e-5 1.0e-7 500 2000
|
||||
|
||||
write_restart system_after_min.rst
|
||||
|
|
@ -0,0 +1,48 @@
|
|||
# -- Init Section --
|
||||
|
||||
include system.in.init
|
||||
|
||||
# -- Atom Definition Section --
|
||||
|
||||
# I you want to be careful, you can minimize the system first. (Try using
|
||||
# "run.in.min" and uncomment the read_restart command in this file below.)
|
||||
# read_restart system_after_min.rst
|
||||
|
||||
read_data system.data
|
||||
|
||||
# -- Settings Section --
|
||||
|
||||
include system.in.settings
|
||||
|
||||
# -- Run Section --
|
||||
|
||||
|
||||
timestep 0.025
|
||||
dump 1 all custom 50000 traj_nvt.lammpstrj id mol type x y z ix iy iz
|
||||
|
||||
# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve".
|
||||
# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.)
|
||||
|
||||
# Keep the chaperonin fixed. Only let the protein move.
|
||||
|
||||
fix fxlan proteins langevin 0.25 0.25 1.0 48279
|
||||
fix fxnve proteins nve
|
||||
|
||||
# Notes:
|
||||
# The temperature is in reduced units and is set to 0.25
|
||||
# which is the folding temperature for the frustrated protein
|
||||
# The inverse-damping-rate "damp" (which has units of time) is set to 1.0,
|
||||
# as it was in the paper. (Hopefully folding times should be similar.)
|
||||
# (See http://lammps.sandia.gov/doc/fix_langevin.html)
|
||||
|
||||
|
||||
thermo_style custom step temp pe etotal press vol epair ebond eangle edihed
|
||||
thermo_modify norm no #(report total energy not energy / num_atoms)
|
||||
thermo 50000 #(time interval for printing out "thermo" data)
|
||||
|
||||
#restart 100000000 restart_nvt
|
||||
|
||||
run 1000000000
|
||||
|
||||
write_restart system_after_nvt.rst
|
||||
|
||||
|
|
@ -0,0 +1,38 @@
|
|||
# This directory demonstrates how to run a long simulation of
|
||||
# the "frustrated" coarse-grained protein in the presence of one
|
||||
# or more coarse-graine small ("mini") chaperones (R=3, h=0.6) as described in:
|
||||
#
|
||||
# AI Jewett and J-E Shea, J. Mol. Biol, Vol 363(5), (2006)
|
||||
# and earlier in:
|
||||
# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
|
||||
#
|
||||
# Because this process takes a long time (even with the help of the chaperone)
|
||||
# I save the data relatively infrequently.
|
||||
#
|
||||
# Note: In the 2006 paper, only one protein and one chaperone was simulated.
|
||||
# In this example, 8 proteins and 8 chaperones were simulated.
|
||||
#
|
||||
# Note: In this case, the chaperones appear to catalyze aggregation.
|
||||
# This is due to an artifact in the protein model. That model
|
||||
# was not designed to study aggregation. However the simulation
|
||||
# is suitable for making pretty pictures (to show off moltemplate).
|
||||
#
|
||||
# -------- REQUIREMENTS: ---------
|
||||
# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC")
|
||||
# http://lammps.sandia.gov/doc/Section_start.html#start_3
|
||||
# 2) It also may require additional features and bug fixes for LAMMPS.
|
||||
# be sure to download and copy the "additional_lammps_code" from
|
||||
# http://moltemplate.org (upper-left corner menu)
|
||||
# 3) Unpack it
|
||||
# 4) copy the .cpp and .h files to the src folding of your lammps installation.
|
||||
# 5) Compile LAMMPS.
|
||||
|
||||
-------------
|
||||
Instructions on how to build LAMMPS input files and
|
||||
run a short simulation are provided in other README files.
|
||||
|
||||
step 1)
|
||||
README_setup.sh
|
||||
|
||||
step2)
|
||||
README_run.sh
|
||||
|
|
@ -0,0 +1,31 @@
|
|||
# You would probably run lammps this way:
|
||||
#
|
||||
# lmp_ubuntu -i run.in.nvt
|
||||
|
||||
# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer
|
||||
# to the input scripts & data files you created earlier when you ran moltemplate
|
||||
# system.in.init, system.in.settings, system.data
|
||||
|
||||
|
||||
|
||||
|
||||
# -----------------------------------
|
||||
|
||||
|
||||
|
||||
LAMMPS_COMMAND="lmp_ubuntu"
|
||||
|
||||
# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps
|
||||
# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary.
|
||||
|
||||
# Run lammps using the following 3 commands:
|
||||
|
||||
"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL)
|
||||
"$LAMMPS_COMMAND" -i run.in.nvt # production run
|
||||
|
||||
# Alternately, if you have MPI installed, try something like this:
|
||||
|
||||
#NUMPROCS=4
|
||||
#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL)
|
||||
#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run
|
||||
|
||||
|
|
@ -0,0 +1,24 @@
|
|||
# Use these commands to generate the LAMMPS input script and data file
|
||||
# (and other auxilliary files):
|
||||
|
||||
|
||||
# Create LAMMPS input files this way:
|
||||
cd moltemplate_files
|
||||
|
||||
# run moltemplate
|
||||
|
||||
moltemplate.sh -overlay-dihdedrals system.lt
|
||||
|
||||
# This will generate various files with names ending in *.in* and *.data.
|
||||
# These files are the input files directly read by LAMMPS. Move them to
|
||||
# the parent directory (or wherever you plan to run the simulation).
|
||||
|
||||
mv -f system.in* system.data ../
|
||||
cp -r table*.dat ../
|
||||
|
||||
# Optional:
|
||||
# The "./output_ttree/" directory is full of temporary files generated by
|
||||
# moltemplate. They can be useful for debugging, but are usually thrown away.
|
||||
rm -rf output_ttree/
|
||||
|
||||
cd ../
|
||||
|
|
@ -0,0 +1,87 @@
|
|||
|
||||
------- To view a lammps trajectory in VMD --------
|
||||
|
||||
|
||||
1) Build a PSF file for use in viewing with VMD.
|
||||
|
||||
This step works with VMD 1.9 and topotools 1.2.
|
||||
(Older versions, like VMD 1.8.6, don't support this.)
|
||||
|
||||
|
||||
a) Start VMD
|
||||
b) Menu Extensions->Tk Console
|
||||
c) Enter:
|
||||
|
||||
(I assume that the the DATA file is called "system.data")
|
||||
|
||||
topo readlammpsdata system.data full
|
||||
animate write psf system.psf
|
||||
|
||||
2)
|
||||
|
||||
Later, to Load a trajectory in VMD:
|
||||
|
||||
Start VMD
|
||||
Select menu: File->New Molecule
|
||||
-Browse to select the PSF file you created above, and load it.
|
||||
(Don't close the window yet.)
|
||||
-Browse to select the trajectory file.
|
||||
If necessary, for "file type" select: "LAMMPS Trajectory"
|
||||
Load it.
|
||||
|
||||
---- A note on trajectory format: -----
|
||||
If the trajectory is a DUMP file, then make sure the it contains the
|
||||
information you need for pbctools (see below. I've been using this
|
||||
command in my LAMMPS scripts to create the trajectories:
|
||||
|
||||
dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
|
||||
|
||||
It's a good idea to use an atom_style which supports molecule-ID numbers
|
||||
so that you can assign a molecule-ID number to each atom. (I think this
|
||||
is needed to wrap atom coordinates without breaking molecules in half.)
|
||||
|
||||
Of course, you don't have to save your trajectories in DUMP format,
|
||||
(other formats like DCD work fine) I just mention dump files
|
||||
because these are the files I'm familiar with.
|
||||
|
||||
3) ----- Wrap the coordinates to the unit cell
|
||||
(without cutting the molecules in half)
|
||||
|
||||
a) Start VMD
|
||||
b) Load the trajectory in VMD (see above)
|
||||
c) Menu Extensions->Tk Console
|
||||
d) Try entering these commands:
|
||||
|
||||
pbc wrap -compound res -all
|
||||
pbc box
|
||||
|
||||
----- Optional ----
|
||||
Sometimes the solvent or membrane obscures the view of the solute.
|
||||
It can help to shift the location of the periodic boundary box
|
||||
To shift the box in the y direction (for example) do this:
|
||||
|
||||
pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
|
||||
pbc box -shiftcenterrel {0.0 0.15 0.0}
|
||||
|
||||
Distances are measured in units of box-length fractions, not Angstroms.
|
||||
|
||||
Alternately if you have a solute whose atoms are all of type 1,
|
||||
then you can also try this to center the box around it:
|
||||
|
||||
pbc wrap -sel type=1 -all -centersel type=2 -center com
|
||||
|
||||
4)
|
||||
You should check if your periodic boundary conditions are too small.
|
||||
To do that:
|
||||
select Graphics->Representations menu option
|
||||
click on the "Periodic" tab, and
|
||||
click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
|
||||
|
||||
5) Optional: If you like, change the atom types in the PSF file so
|
||||
that VMD recognizes the atom types, use something like:
|
||||
|
||||
sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
|
||||
sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
|
||||
sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
|
||||
|
||||
(If you do this, it might effect step 2 above.)
|
||||
|
|
@ -0,0 +1,476 @@
|
|||
PSF
|
||||
|
||||
1 !NTITLE
|
||||
REMARKS VMD generated structure x-plor psf file
|
||||
|
||||
224 !NATOM
|
||||
1 1 2 2 0.000000 1.0000 0
|
||||
2 1 1 1 0.000000 1.0000 0
|
||||
3 1 2 2 0.000000 1.0000 0
|
||||
4 1 1 1 0.000000 1.0000 0
|
||||
5 1 2 2 0.000000 1.0000 0
|
||||
6 1 1 1 0.000000 1.0000 0
|
||||
7 1 3 3 0.000000 1.0000 0
|
||||
8 1 3 3 0.000000 1.0000 0
|
||||
9 1 1 1 0.000000 1.0000 0
|
||||
10 1 2 2 0.000000 1.0000 0
|
||||
11 1 1 1 0.000000 1.0000 0
|
||||
12 1 2 2 0.000000 1.0000 0
|
||||
13 1 1 1 0.000000 1.0000 0
|
||||
14 1 2 2 0.000000 1.0000 0
|
||||
15 1 3 3 0.000000 1.0000 0
|
||||
16 1 3 3 0.000000 1.0000 0
|
||||
17 1 3 3 0.000000 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
|
||||
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 30 KiB |
Binary file not shown.
|
After Width: | Height: | Size: 26 KiB |
|
|
@ -0,0 +1,216 @@
|
|||
# This file defines the "frustrated" coarse-grained protein model used in:
|
||||
# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
|
||||
# (http://www.pnas.org/content/101/36/13192)
|
||||
|
||||
|
||||
1beadFrustrated {
|
||||
|
||||
# There are 3 atom types (referred to above as B, L, and N)
|
||||
# Define their masses:
|
||||
|
||||
write_once("Data Masses") {
|
||||
@atom:B 1.0
|
||||
@atom:L 1.0
|
||||
@atom:N 1.0
|
||||
}
|
||||
|
||||
# AtomID MoleculeID AtomType Charge X Y Z
|
||||
|
||||
write('Data Atoms') {
|
||||
$atom:a1 $mol @atom:L 0.0 -0.92636654 -1.8409904 -2.1482679
|
||||
$atom:a2 $mol @atom:B 0.0 -0.57313354 -1.0670787 -1.6182341
|
||||
$atom:a3 $mol @atom:L 0.0 -0.85707399 -1.2358703 -0.69350966
|
||||
$atom:a4 $mol @atom:B 0.0 -0.44231274 -0.4584993 -0.23418709
|
||||
$atom:a5 $mol @atom:L 0.0 -0.75081182 -0.62868078 0.69786737
|
||||
$atom:a6 $mol @atom:B 0.0 -0.36201977 0.11619615 1.2249098
|
||||
$atom:a7 $mol @atom:N 0.0 -0.63708237 -0.15973084 2.1723919
|
||||
$atom:a8 $mol @atom:N 0.0 0.20516047 0.10417157 2.624901
|
||||
$atom:a9 $mol @atom:B 0.0 0.57223743 0.44728103 1.7695617
|
||||
$atom:a10 $mol @atom:L 0.0 0.77646279 -0.40630393 1.3168043
|
||||
$atom:a11 $mol @atom:B 0.0 0.45475664 -0.2077937 0.40045721
|
||||
$atom:a12 $mol @atom:L 0.0 0.72712495 -1.0397637 -0.087614951
|
||||
$atom:a13 $mol @atom:B 0.0 0.36971183 -0.85840501 -0.9933019
|
||||
$atom:a14 $mol @atom:L 0.0 0.74784336 -1.5700415 -1.5859217
|
||||
$atom:a15 $mol @atom:N 0.0 0.43423905 -1.2758917 -2.4853429
|
||||
$atom:a16 $mol @atom:N 0.0 0.70583191 -0.30726921 -2.4987711
|
||||
$atom:a17 $mol @atom:N 0.0 -0.091688915 0.23323014 -2.2051358
|
||||
$atom:a18 $mol @atom:B 0.0 -0.34243283 -0.035822049 -1.2644719
|
||||
$atom:a19 $mol @atom:B 0.0 0.41961247 0.18475451 -0.65971014
|
||||
$atom:a20 $mol @atom:L 0.0 0.51968465 1.1546791 -0.77877053
|
||||
$atom:a21 $mol @atom:L 0.0 -0.40827985 1.2765273 -0.52550748
|
||||
$atom:a22 $mol @atom:B 0.0 -0.368141 0.58090904 0.19152224
|
||||
$atom:a23 $mol @atom:B 0.0 0.40327249 0.86101769 0.7336255
|
||||
$atom:a24 $mol @atom:L 0.0 0.22707289 1.8326235 0.89673346
|
||||
$atom:a25 $mol @atom:L 0.0 -0.66500182 1.7285809 1.2783166
|
||||
$atom:a26 $mol @atom:B 0.0 -0.39205603 1.0475436 1.9328097
|
||||
$atom:a27 $mol @atom:L 0.0 0.25339027 1.5246265 2.5388463
|
||||
}
|
||||
|
||||
# bond-ID bond-Type atom-ID atom-ID
|
||||
|
||||
write('Data Bonds') {
|
||||
$bond:b1 @bond:backbone $atom:a1 $atom:a2
|
||||
$bond:b2 @bond:backbone $atom:a2 $atom:a3
|
||||
$bond:b3 @bond:backbone $atom:a3 $atom:a4
|
||||
$bond:b4 @bond:backbone $atom:a4 $atom:a5
|
||||
$bond:b5 @bond:backbone $atom:a5 $atom:a6
|
||||
$bond:b6 @bond:backbone $atom:a6 $atom:a7
|
||||
$bond:b7 @bond:backbone $atom:a7 $atom:a8
|
||||
$bond:b8 @bond:backbone $atom:a8 $atom:a9
|
||||
$bond:b9 @bond:backbone $atom:a9 $atom:a10
|
||||
$bond:b10 @bond:backbone $atom:a10 $atom:a11
|
||||
$bond:b11 @bond:backbone $atom:a11 $atom:a12
|
||||
$bond:b12 @bond:backbone $atom:a12 $atom:a13
|
||||
$bond:b13 @bond:backbone $atom:a13 $atom:a14
|
||||
$bond:b14 @bond:backbone $atom:a14 $atom:a15
|
||||
$bond:b15 @bond:backbone $atom:a15 $atom:a16
|
||||
$bond:b16 @bond:backbone $atom:a16 $atom:a17
|
||||
$bond:b17 @bond:backbone $atom:a17 $atom:a18
|
||||
$bond:b18 @bond:backbone $atom:a18 $atom:a19
|
||||
$bond:b19 @bond:backbone $atom:a19 $atom:a20
|
||||
$bond:b20 @bond:backbone $atom:a20 $atom:a21
|
||||
$bond:b21 @bond:backbone $atom:a21 $atom:a22
|
||||
$bond:b22 @bond:backbone $atom:a22 $atom:a23
|
||||
$bond:b23 @bond:backbone $atom:a23 $atom:a24
|
||||
$bond:b24 @bond:backbone $atom:a24 $atom:a25
|
||||
$bond:b25 @bond:backbone $atom:a25 $atom:a26
|
||||
$bond:b26 @bond:backbone $atom:a26 $atom:a27
|
||||
}
|
||||
|
||||
# (3-body) Angles are specified below
|
||||
|
||||
# (4-body) Dihedrals must be defined explicitly for every quartet of atoms.
|
||||
# (These interactions are not determined by atom type.)
|
||||
|
||||
# dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID
|
||||
|
||||
write('Data Dihedrals') {
|
||||
|
||||
$dihedral:d1 @dihedral:beta $atom:a1 $atom:a2 $atom:a3 $atom:a4
|
||||
$dihedral:d2 @dihedral:beta $atom:a2 $atom:a3 $atom:a4 $atom:a5
|
||||
$dihedral:d3 @dihedral:beta $atom:a3 $atom:a4 $atom:a5 $atom:a6
|
||||
$dihedral:d4 @dihedral:beta $atom:a4 $atom:a5 $atom:a6 $atom:a7
|
||||
|
||||
# Dihedral angle forces in the turn regions were switched off
|
||||
# (in this model) so just I comment them out (and \ the variable names).
|
||||
# \$dihedral:d5 \@dihedral:turn $atom:a5 $atom:a6 $atom:a7 $atom:a8
|
||||
# \$dihedral:d6 \@dihedral:turn $atom:a6 $atom:a7 $atom:a8 $atom:a9
|
||||
# \$dihedral:d7 \@dihedral:turn $atom:a7 $atom:a8 $atom:a9 $atom:a10
|
||||
|
||||
$dihedral:d8 @dihedral:beta $atom:a8 $atom:a9 $atom:a10 $atom:a11
|
||||
$dihedral:d9 @dihedral:beta $atom:a9 $atom:a10 $atom:a11 $atom:a12
|
||||
$dihedral:d10 @dihedral:beta $atom:a10 $atom:a11 $atom:a12 $atom:a13
|
||||
$dihedral:d11 @dihedral:beta $atom:a11 $atom:a12 $atom:a13 $atom:a14
|
||||
$dihedral:d12 @dihedral:beta $atom:a12 $atom:a13 $atom:a14 $atom:a15
|
||||
|
||||
# Dihedral angle forces in the turn regions were switched off
|
||||
# (in this model) so just I comment them out (and \ the variable names).
|
||||
# \$dihedral:d13 \@dihedral:turn $atom:a13 $atom:a14 $atom:a15 $atom:a16
|
||||
# \$dihedral:d14 \@dihedral:turn $atom:a14 $atom:a15 $atom:a16 $atom:a17
|
||||
|
||||
$dihedral:d15 @dihedral:alpha $atom:a15 $atom:a16 $atom:a17 $atom:a18
|
||||
$dihedral:d16 @dihedral:alpha $atom:a16 $atom:a17 $atom:a18 $atom:a19
|
||||
$dihedral:d17 @dihedral:alpha $atom:a17 $atom:a18 $atom:a19 $atom:a20
|
||||
$dihedral:d18 @dihedral:alpha $atom:a18 $atom:a19 $atom:a20 $atom:a21
|
||||
$dihedral:d19 @dihedral:alpha $atom:a19 $atom:a20 $atom:a21 $atom:a22
|
||||
$dihedral:d20 @dihedral:alpha $atom:a20 $atom:a21 $atom:a22 $atom:a23
|
||||
$dihedral:d21 @dihedral:alpha $atom:a21 $atom:a22 $atom:a23 $atom:a24
|
||||
$dihedral:d22 @dihedral:alpha $atom:a22 $atom:a23 $atom:a24 $atom:a25
|
||||
$dihedral:d23 @dihedral:alpha $atom:a23 $atom:a24 $atom:a25 $atom:a26
|
||||
$dihedral:d24 @dihedral:alpha $atom:a24 $atom:a25 $atom:a26 $atom:a27
|
||||
}
|
||||
|
||||
# All consecutively bonded triplets of atoms same 3-body bond-angle
|
||||
# interaction parameters. Of coarse, we could specify them all explicitly
|
||||
# (as we did for the dihedrals above), but I wanted to show how to specify
|
||||
# angles by atom type instead. (You can do this for dihedrals & impropers
|
||||
# also.)
|
||||
|
||||
# angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type
|
||||
|
||||
write_once('Data Angles By Type') {
|
||||
@angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:*
|
||||
}
|
||||
|
||||
# (The "*" is a wildcard character. I use "*" to denote any atom-type or
|
||||
# bond-type which is defined within the current namespace: 1beadFrustrated)
|
||||
|
||||
|
||||
# 2-body (non-bonded) interactions:
|
||||
#
|
||||
# Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6)
|
||||
#
|
||||
# i j pairstylename eps sig K L
|
||||
#
|
||||
write_once("In Settings") {
|
||||
pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1
|
||||
pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0
|
||||
pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0
|
||||
pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1
|
||||
pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0
|
||||
pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0
|
||||
}
|
||||
|
||||
|
||||
# 2-body (bonded) interactions:
|
||||
#
|
||||
# Ubond(r) = (k/2)*(r-0)^2
|
||||
#
|
||||
# The corresponding command is:
|
||||
#
|
||||
# bond-Type bondstylename k r0
|
||||
|
||||
write_once("In Settings") {
|
||||
bond_coeff @bond:backbone harmonic 100.0 1.0
|
||||
}
|
||||
|
||||
# 3-body interactions in this example are listed by atomType and bondType
|
||||
# The atomIDs involved are determined automatically. The forumula used is:
|
||||
#
|
||||
# Uangle(theta) = (k/2)*(theta-theta0)^2
|
||||
# (k in kcal/mol/rad^2, theta0 in degrees)
|
||||
#
|
||||
# angle-Type anglestylename k theta0
|
||||
|
||||
write_once("In Settings") {
|
||||
angle_coeff @angle:backbone harmonic 13.3333333333 105.0
|
||||
}
|
||||
|
||||
|
||||
# We use tabular dihedral potentials to implement the dihedral forces.
|
||||
# (Actually there is a way to use Fourier series, using multiple charmm
|
||||
# style dihedral interactions, but it's slower and messier.)
|
||||
|
||||
write_once("In Settings") {
|
||||
# style file keyword
|
||||
dihedral_coeff @dihedral:alpha table table_dihedral_frustrated.dat FRUSTRATED_ALPHA
|
||||
dihedral_coeff @dihedral:beta table table_dihedral_frustrated.dat FRUSTRATED_BETA
|
||||
# No need to specify dihedral interactions in the turn regions. (none exist)
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
# Optional: define the atoms in the "proteins" group
|
||||
group proteins type @atom:B
|
||||
group proteins type @atom:L
|
||||
group proteins type @atom:N
|
||||
}
|
||||
|
||||
# LAMMPS has many available force field styles (and atom styles).
|
||||
# Here, we pick the ones which work well for this molecular model:
|
||||
|
||||
write_once("In Init") {
|
||||
# --- Default options for the "1BeadFrustrated" protein model ---
|
||||
# --- (These can be overridden later.) ---
|
||||
units lj
|
||||
atom_style full
|
||||
bond_style hybrid harmonic
|
||||
angle_style hybrid harmonic
|
||||
dihedral_style hybrid table spline 360
|
||||
pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0
|
||||
pair_modify mix arithmetic
|
||||
special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions)
|
||||
}
|
||||
|
||||
} # 1beadFrustrated
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,85 @@
|
|||
import "1beadFrustrated.lt"
|
||||
|
||||
|
||||
# Alternate starting conformation (same molecule):
|
||||
|
||||
|
||||
1beadMisfolded inherits 1beadFrustrated {
|
||||
|
||||
# This molecule "inherits" all of its features from "1beadFrustrated".
|
||||
# Here we override the atomic positions with new coordinates:
|
||||
|
||||
# AtomID MoleculeID AtomType Charge X Y Z
|
||||
|
||||
write("Data Atoms") {
|
||||
$atom:a1 $mol @atom:L 0.0 -0.69801399 -0.22114168 -1.9464876
|
||||
$atom:a2 $mol @atom:B 0.0 -0.40921658 -0.027063664 -1.0033251
|
||||
$atom:a3 $mol @atom:L 0.0 0.10259348 0.80836418 -1.0737085
|
||||
$atom:a4 $mol @atom:B 0.0 0.25857916 1.0054984 -0.11621451
|
||||
$atom:a5 $mol @atom:L 0.0 0.8258629 1.8325549 -0.18529135
|
||||
$atom:a6 $mol @atom:B 0.0 0.91366257 2.1950317 0.74175977
|
||||
$atom:a7 $mol @atom:N 0.0 1.4399539 1.554238 1.2994409
|
||||
$atom:a8 $mol @atom:N 0.0 0.73372573 1.0161012 1.7397275
|
||||
$atom:a9 $mol @atom:B 0.0 0.26608782 0.65302497 0.94353938
|
||||
$atom:a10 $mol @atom:L 0.0 0.97442305 0.13574211 0.50586398
|
||||
$atom:a11 $mol @atom:B 0.0 0.35889617 -0.18247555 -0.1764186
|
||||
$atom:a12 $mol @atom:L 0.0 0.87151735 -0.77260824 -0.75240916
|
||||
$atom:a13 $mol @atom:B 0.0 0.047726486 -1.0530682 -1.1902704
|
||||
$atom:a14 $mol @atom:L 0.0 0.34530697 -1.7476773 -1.8393331
|
||||
$atom:a15 $mol @atom:N 0.0 0.65865186 -2.45948 -1.2167056
|
||||
$atom:a16 $mol @atom:N 0.0 -0.16534524 -2.6219442 -0.67112167
|
||||
$atom:a17 $mol @atom:N 0.0 -0.010590421 -2.2445242 0.24748633
|
||||
$atom:a18 $mol @atom:B 0.0 0.18135771 -1.2564919 0.1767523
|
||||
$atom:a19 $mol @atom:B 0.0 -0.57472665 -0.82852797 -0.27027791
|
||||
$atom:a20 $mol @atom:L 0.0 -1.3967448 -1.0516787 0.24247346
|
||||
$atom:a21 $mol @atom:L 0.0 -1.003428 -0.85642681 1.1107555
|
||||
$atom:a22 $mol @atom:B 0.0 -0.25156735 -0.3182346 0.74262946
|
||||
$atom:a23 $mol @atom:B 0.0 -0.61751956 0.30115562 0.070426493
|
||||
$atom:a24 $mol @atom:L 0.0 -1.3347934 0.83310182 0.52625934
|
||||
$atom:a25 $mol @atom:L 0.0 -0.83315257 1.270904 1.2564086
|
||||
$atom:a26 $mol @atom:B 0.0 -0.10469759 1.6988523 0.72597181
|
||||
$atom:a27 $mol @atom:L 0.0 -0.57854905 2.3367737 0.11206868
|
||||
}
|
||||
|
||||
} # 1beadMisfolded
|
||||
|
||||
|
||||
1beadUnfolded inherits 1beadFrustrated {
|
||||
|
||||
# This molecule "inherits" all of its features from "1beadFrustrated"
|
||||
# Here we override the atomic positions with new coordinates:
|
||||
|
||||
# AtomID MoleculeID AtomType Charge X Y Z
|
||||
|
||||
write('Data Atoms') {
|
||||
$atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0
|
||||
$atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8
|
||||
$atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8
|
||||
$atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0
|
||||
$atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0
|
||||
$atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8
|
||||
$atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8
|
||||
$atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0
|
||||
$atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0
|
||||
$atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8
|
||||
$atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8
|
||||
$atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0
|
||||
$atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0
|
||||
$atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8
|
||||
$atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8
|
||||
$atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2
|
||||
$atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2
|
||||
$atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6
|
||||
$atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6
|
||||
$atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2
|
||||
$atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2
|
||||
$atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6
|
||||
$atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6
|
||||
$atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2
|
||||
$atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2
|
||||
$atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6
|
||||
$atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6
|
||||
}
|
||||
|
||||
} # 1beadUnfolded
|
||||
|
||||
|
|
@ -0,0 +1,87 @@
|
|||
#!/usr/bin/env python
|
||||
|
||||
# Calculate a table of pairwise energies and forces between atoms in the
|
||||
# protein and a chaperone provided in the supplemental materials section of:
|
||||
# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
|
||||
# This is stored in a tabulated force field with a singularity at a distance R.
|
||||
#
|
||||
# To calculate the table for interaction between
|
||||
# ...the chaperone and a hydrophobic bead (2004 PNAS paper), use this table:
|
||||
# ./calc_chaperone_table.py 1.0 1.0 6.0 0.475 0.0 5.9 1181
|
||||
# ...the chaperone and a hydrophilic bead (2004 PNAS paper), use this table:
|
||||
# ./calc_chaperone_table.py 1.0 1.0 6.0 0.0 0.0 5.9 1181
|
||||
# ...the chaperone and a hydrophobic bead (2006 JMB paper), use this table:
|
||||
# ./calc_chaperone_table.py 1.0 1.0 3.0 0.60 3.1 8.0 981 True
|
||||
# ...the chaperone and a hydrophilic bead (2006 JMB paper), use this table:
|
||||
# ./calc_chaperone_table.py 1.0 1.0 3.0 0.0 3.1 8.0 981 True
|
||||
|
||||
from math import *
|
||||
import sys
|
||||
|
||||
def U(r, eps, sigma, R, h):
|
||||
#print('r='+str(r)+' eps='+str(eps)+' s='+str(sigma)+' R='+str(R)+' h='+str(h))
|
||||
# Formula is undefined at r=0, but you can take the limit:
|
||||
if r <= 0:
|
||||
return 4.0*pi*R*R*4.0*eps*(pow((sigma/R), 12.0)
|
||||
- h*pow((sigma/R), 6.0))
|
||||
xp = sigma/(r+R)
|
||||
xm = sigma/(r-R)
|
||||
term10 = pow(xm, 10.0) - pow(xp, 10.0)
|
||||
term4 = pow(xm, 4.0) - pow(xp, 4.0)
|
||||
return 4.0*pi*eps*(R/r) * (0.2*term10 - 0.5*h*term4)
|
||||
|
||||
def F(r, eps, sigma, R, h):
|
||||
# Formula is undefined at r=0, but you can take the limit:
|
||||
if r <= 0:
|
||||
return 0.0
|
||||
product_term_a = U(r, eps, sigma, R, h) / r
|
||||
ixp = (r+R)/sigma
|
||||
ixm = (r-R)/sigma
|
||||
dix_dr = 1.0/sigma
|
||||
term10 = (10.0/sigma)*(pow(ixm, -11.0) - pow(ixp, -11.0))
|
||||
term4 = (4.0/sigma)*(pow(ixm, -5.0) - pow(ixp, -5.0))
|
||||
product_term_b = 4.0*eps*pi*(R/r) * (0.2*term10 - 0.5*h*term4)
|
||||
return product_term_a + product_term_b
|
||||
|
||||
|
||||
class InputError(Exception):
|
||||
""" A generic exception object containing a string for error reporting.
|
||||
|
||||
"""
|
||||
def __init__(self, err_msg):
|
||||
self.err_msg = err_msg
|
||||
def __str__(self):
|
||||
return self.err_msg
|
||||
def __repr__(self):
|
||||
return str(self)
|
||||
|
||||
if len(sys.argv) < 8:
|
||||
sys.stderr.write("Error: expected 7 arguments:\n"
|
||||
"\n"
|
||||
"Usage: "+sys.argv[0]+" epsilon sigma R h rmin rmax N\n\n")
|
||||
sys.exit(-1)
|
||||
|
||||
epsilon = float(sys.argv[1])
|
||||
sigma = float(sys.argv[2])
|
||||
R = float(sys.argv[3])
|
||||
h = float(sys.argv[4])
|
||||
rmin = float(sys.argv[5])
|
||||
rmax = float(sys.argv[6])
|
||||
N = int(sys.argv[7])
|
||||
|
||||
subtract_Urcut = False
|
||||
if len(sys.argv) == 9:
|
||||
subtract_Urcut = True
|
||||
rcut = rmax
|
||||
|
||||
for i in range(0,N):
|
||||
r = rmin + i*(rmax-rmin)/(N-1)
|
||||
U_r = U(r, epsilon, sigma, R, h)
|
||||
F_r = F(r, epsilon, sigma, R, h)
|
||||
if subtract_Urcut:
|
||||
U_r -= U(rcut, epsilon, sigma, R, h)
|
||||
if (r >= rcut) or (i==N-1):
|
||||
U_r = 0.0
|
||||
F_r = 0.0
|
||||
print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))
|
||||
|
||||
|
|
@ -0,0 +1,67 @@
|
|||
#!/usr/bin/env python
|
||||
|
||||
# Calculate a table of dihedral angle interactions used in the alpha-helix
|
||||
# and beta-sheet regions of the frustrated protein model described in
|
||||
# provided in figure 8 of the supplemental materials section of:
|
||||
# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
|
||||
# Note that the "A" and "B" parameters were incorrectly reported to be
|
||||
# 5.4*epsilon and 6.0*epsilon. The values used were 5.6 and 6.0 epsilon.
|
||||
# The phiA and phiB values were 57.29577951308232 degrees (1 rad)
|
||||
# and 180 degrees, respectively. Both expA and expB were 6.0.
|
||||
#
|
||||
# To generate the table used for the alpha-helix (1 degree resolution) use this:
|
||||
# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360
|
||||
# To generate the table used for the beta-sheets (1 degree resolution) use this:
|
||||
# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360
|
||||
#
|
||||
# (If you're curious as to why I set the location of the minima at phi_alpha
|
||||
# to 1.0 radians (57.2957795 degrees), there was no particularly good reason.
|
||||
# I think the correct value turns out to be something closer to 50 degrees.)
|
||||
|
||||
|
||||
from math import *
|
||||
import sys
|
||||
|
||||
|
||||
# The previous version included the repulsive core term
|
||||
def U(phi, A, phiA, expA, B, phiB, expB, use_radians=False):
|
||||
conv_units = pi/180.0
|
||||
if use_radians:
|
||||
conv_units = 1.0
|
||||
termA = pow(cos(0.5*(phi-phiA)*conv_units), expA)
|
||||
termB = pow(cos(0.5*(phi-phiB)*conv_units), expB)
|
||||
return -A*termA - B*termB
|
||||
|
||||
# The previous version included the repulsive core term
|
||||
def F(phi, A, phiA, expA, B, phiB, expB, use_radians=False):
|
||||
conv_units = pi/180.0
|
||||
if use_radians:
|
||||
conv_units = 1.0
|
||||
termA = (0.5*sin(0.5*(phi-phiA)*conv_units) *
|
||||
expA * pow(cos(0.5*(phi-phiA)*conv_units), expA-1.0))
|
||||
termB = (0.5*sin(0.5*(phi-phiB)*conv_units) *
|
||||
expB * pow(cos(0.5*(phi-phiB)*conv_units), expB-1.0))
|
||||
return -conv_units*(A*termA + B*termB)
|
||||
|
||||
if len(sys.argv) != 10:
|
||||
sys.stderr.write("Error: expected 9 arguments:\n"
|
||||
"\n"
|
||||
"Usage: "+sys.argv[0]+" A phiA expA B phiB expB phiMin phiMax N\n\n")
|
||||
sys.exit(-1)
|
||||
|
||||
A = float(sys.argv[1])
|
||||
phiA = float(sys.argv[2])
|
||||
expA = float(sys.argv[3])
|
||||
B = float(sys.argv[4])
|
||||
phiB = float(sys.argv[5])
|
||||
expB = float(sys.argv[6])
|
||||
phi_min = float(sys.argv[7])
|
||||
phi_max = float(sys.argv[8])
|
||||
N = int(sys.argv[9])
|
||||
|
||||
for i in range(0,N):
|
||||
phi = phi_min + i*(phi_max - phi_min)/(N-1)
|
||||
U_phi = U(phi, A, phiA, expA, B, phiB, expB, use_radians=False)
|
||||
F_phi = F(phi, A, phiA, expA, B, phiB, expB, use_radians=False)
|
||||
print(str(i+1)+' '+str(phi)+' '+str(U_phi)+' '+str(F_phi))
|
||||
|
||||
|
|
@ -0,0 +1,41 @@
|
|||
# Here we define a trivial molecule containing only one particle.
|
||||
|
||||
Minichaperone {
|
||||
|
||||
# atomID molID atomType charge x y z
|
||||
|
||||
write("Data Atoms") {
|
||||
$atom:C $mol @atom:C 0.0 0.0 0.0 0.0
|
||||
}
|
||||
|
||||
write_once("Data Masses") {
|
||||
@atom:C 100.0
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
# If for some reason there are multiple chaperones present,
|
||||
# I assume that they interact repulsively (hence, L=0)
|
||||
|
||||
# i j pairStyle eps sig K L
|
||||
|
||||
pair_coeff @atom:C @atom:C lj/charmm/coul/charmm/inter 1.0 3.0 1 0
|
||||
|
||||
# Optional: define the atoms in the "chaperonins" group:
|
||||
# (Defining a group for the chaperone makes it easy to immobilize it later.)
|
||||
|
||||
group chaperones type @atom:C
|
||||
}
|
||||
|
||||
# Specify which pair_styles, and atom styles work well with
|
||||
# this model. (Again this can be overridden later.)
|
||||
|
||||
write_once("In Init") {
|
||||
units lj
|
||||
atom_style full
|
||||
pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 8.0 9.0
|
||||
}
|
||||
|
||||
} # Minichaperone
|
||||
|
||||
# We have not specified how this particle interacts with other particles
|
||||
# besides itself. Later on you must do this.
|
||||
|
|
@ -0,0 +1,72 @@
|
|||
write_once("Data Boundary") {
|
||||
0.0 80.0 xlo xhi
|
||||
0.0 80.0 ylo yhi
|
||||
0.0 80.0 zlo zhi
|
||||
}
|
||||
|
||||
|
||||
import "1beadFrustrated_variants.lt"
|
||||
import "minichaperone.lt"
|
||||
|
||||
|
||||
# Create 8 proteins and 8 chaperones (2x2x2 array):
|
||||
# NOTE: Below I create multiple proteins and multiple chaperones
|
||||
# to see what would happen. (I suspect nothing good. In the
|
||||
# 2006 paper, only 1 protein and 1 chaperone were present.)
|
||||
|
||||
|
||||
proteins = new 1beadUnfolded [2].move(40,0,0)
|
||||
[2].move(0,40,0)
|
||||
[2].move(0,0,40)
|
||||
|
||||
chaperones = new Minichaperone [2].move(40,0,0)
|
||||
[2].move(0,40,0)
|
||||
[2].move(0,0,40)
|
||||
|
||||
proteins[*][*][*].move(20,20,20) # to avoid overlap with the chaperones
|
||||
|
||||
|
||||
|
||||
# If you only want 1 protein and 1 chaperone
|
||||
# then replace the lines above with:
|
||||
#
|
||||
# protein = new 1beadMisfolded
|
||||
# chaperone = new Minichaperone
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
# ---- Now define interactions between the atoms in the protein ----
|
||||
# ---- (named "B", "L", "N") and the atom which represents the ----
|
||||
# ---- chaperone ("c"). These interactions are tabulated. ----
|
||||
|
||||
write_once("In Settings") {
|
||||
pair_coeff @atom:Minichaperone/C @atom:1beadFrustrated/B table table_minichaperone_h=0.6.dat CH_H0.6
|
||||
pair_coeff @atom:Minichaperone/C @atom:1beadFrustrated/L table table_minichaperone_h=0.dat CH_H0
|
||||
pair_coeff @atom:Minichaperone/C @atom:1beadFrustrated/N table table_minichaperone_h=0.dat CH_H0
|
||||
}
|
||||
|
||||
# Note: If you want purely repulsive spheres (crowding, h=0.0)
|
||||
# instead of an attractive "hydrophobic" chaperone (h=0.6)
|
||||
# then replace "table_minichaperone_h=0_6.dat CH_H0_6"
|
||||
# with "table_minichaperone_h=0.dat CH_H0"
|
||||
# (... or just use an ordinary Lennard-Jones interaction
|
||||
# with sigma = 6.0 and epsilon near 0.0)
|
||||
|
||||
|
||||
# LAMMPS has many available force field styles (and atom styles). Here we
|
||||
# select the ones which work well for the full combine system. (This should
|
||||
# override any settings made in "1beadFrustrated.lt" or "minichaperone.lt")
|
||||
|
||||
|
||||
write_once("In Init") {
|
||||
units lj
|
||||
atom_style full
|
||||
bond_style hybrid harmonic
|
||||
angle_style hybrid harmonic
|
||||
dihedral_style hybrid table spline 360
|
||||
pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 table spline 981
|
||||
pair_modify mix arithmetic
|
||||
special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions)
|
||||
}
|
||||
|
|
@ -0,0 +1,735 @@
|
|||
# Table of the potential and its negative derivative for frustrated alpha helix
|
||||
# (Note: Derivatives are in units of energy/radians, not energy/degrees.)
|
||||
# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360
|
||||
|
||||
FRUSTRATED_ALPHA
|
||||
N 360 DEGREES
|
||||
|
||||
1 0.0 -2.74081145103 0.0783990792662
|
||||
2 1.0 -2.81950869101 0.0789852583442
|
||||
3 2.0 -2.89876136749 0.0795096391909
|
||||
4 3.0 -2.97850675562 0.0799703813963
|
||||
5 4.0 -3.05868032959 0.0803657243943
|
||||
6 5.0 -3.13921584545 0.0806939935737
|
||||
7 6.0 -3.22004543014 0.0809536062381
|
||||
8 7.0 -3.30109967628 0.0811430773977
|
||||
9 8.0 -3.38230774267 0.0812610253741
|
||||
10 9.0 -3.46359746038 0.0813061772009
|
||||
11 10.0 -3.54489544401 0.0812773738039
|
||||
12 11.0 -3.62612720812 0.0811735749433
|
||||
13 12.0 -3.70721728841 0.0809938639029
|
||||
14 13.0 -3.78808936748 0.080737451911
|
||||
15 14.0 -3.86866640485 0.0804036822781
|
||||
16 15.0 -3.94887077101 0.0799920342374
|
||||
17 16.0 -4.02862438516 0.0795021264757
|
||||
18 17.0 -4.10784885622 0.0789337203415
|
||||
19 18.0 -4.18646562704 0.0782867227197
|
||||
20 19.0 -4.26439612115 0.0775611885609
|
||||
21 20.0 -4.34156189202 0.0767573230567
|
||||
22 21.0 -4.41788477419 0.0758754834523
|
||||
23 22.0 -4.49328703609 0.0749161804868
|
||||
24 23.0 -4.56769153408 0.0738800794563
|
||||
25 24.0 -4.64102186743 0.0727680008923
|
||||
26 25.0 -4.71320253365 0.0715809208518
|
||||
27 26.0 -4.78415908407 0.0703199708131
|
||||
28 27.0 -4.85381827903 0.0689864371778
|
||||
29 28.0 -4.92210824234 0.067581760373
|
||||
30 29.0 -4.98895861476 0.0661075335571
|
||||
31 30.0 -5.05430070586 0.0645655009259
|
||||
32 31.0 -5.11806764409 0.0629575556235
|
||||
33 32.0 -5.18019452449 0.061285737258
|
||||
34 33.0 -5.24061855376 0.0595522290273
|
||||
35 34.0 -5.29927919225 0.0577593544584
|
||||
36 35.0 -5.3561182925 0.0559095737673
|
||||
37 36.0 -5.41108023395 0.0540054798439
|
||||
38 37.0 -5.46411205346 0.0520497938726
|
||||
39 38.0 -5.51516357127 0.0500453605949
|
||||
40 39.0 -5.56418751203 0.0479951432253
|
||||
41 40.0 -5.61113962059 0.0459022180302
|
||||
42 41.0 -5.65597877221 0.0437697685824
|
||||
43 42.0 -5.69866707689 0.0416010797029
|
||||
44 43.0 -5.7391699774 0.0393995311046
|
||||
45 44.0 -5.77745634094 0.0371685907508
|
||||
46 45.0 -5.81349854393 0.034911807945
|
||||
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|
||||
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
|
||||
|
|
@ -0,0 +1,988 @@
|
|||
# Interaction between a chaperone wall and hydrophobic ("B") beads (h=0.6)
|
||||
# Generated using:
|
||||
# generate_tables/calc_chaperone_table.py 1.0 1.0 3.0 0.60 3.1 8.0 981 True
|
||||
|
||||
CH_H0.6
|
||||
N 981 R 3.1 8.0
|
||||
|
||||
1 3.1 24321971157.7 2.4400451019e+12
|
||||
2 3.105 14907528428.0 1.42456746092e+12
|
||||
3 3.11 9347010266.92 8.52735030437e+11
|
||||
4 3.115 5983057175.03 5.22187648991e+11
|
||||
5 3.12 3902942155.05 3.26496996649e+11
|
||||
6 3.125 2590648415.38 2.0808159227e+11
|
||||
7 3.13 1747350825.1 1.34970444886e+11
|
||||
8 3.135 1196139798.89 88984974583.5
|
||||
9 3.14 830130182.341 59559787515.6
|
||||
10 3.145 583518174.975 40428507749.3
|
||||
11 3.15 415078797.287 27803974550.9
|
||||
12 3.155 298562827.719 19356989964.4
|
||||
13 3.16 217001769.743 13631486848.5
|
||||
14 3.165 159270305.159 9703243449.66
|
||||
15 3.17 117976881.962 6977184032.49
|
||||
16 3.175 88149161.6455 5064988683.98
|
||||
17 3.18 66402860.1298 3710042118.5
|
||||
18 3.185 50409022.6215 2740737360.59
|
||||
19 3.19 38548170.6708 2041021063.98
|
||||
20 3.195 29683036.1074 1531572773.33
|
||||
21 3.2 23007502.8905 1157631256.92
|
||||
22 3.205 17945109.6836 881028781.898
|
||||
23 3.21 14080149.2893 674921399.554
|
||||
24 3.215 11110438.2418 520266326.167
|
||||
25 3.22 8814639.75879 403443800.764
|
||||
26 3.225 7029455.47123 314636408.027
|
||||
27 3.23 5633571.16439 246714657.082
|
||||
28 3.235 4536265.59262 194464091.949
|
||||
29 3.24 3669265.83647 154044868.616
|
||||
30 3.245 2980881.1453 122610915.077
|
||||
31 3.25 2431748.15466 98039536.8272
|
||||
32 3.255 1991724.07297 78738058.3506
|
||||
33 3.26 1637603.46485 63504600.2322
|
||||
34 3.265 1351429.90872 51427172.534
|
||||
35 3.27 1119240.11293 41810074.9071
|
||||
36 3.275 930124.378436 34119886.2947
|
||||
37 3.28 775519.857832 27945597.578
|
||||
38 3.285 648676.115123 22969017.4933
|
||||
39 3.29 544248.919174 18942684.9889
|
||||
40 3.295 457989.984944 15673297.5619
|
||||
41 3.3 386508.875651 13009215.1485
|
||||
42 3.305 327089.446276 10830991.226
|
||||
43 3.31 277547.709074 9044163.93118
|
||||
44 3.315 236121.303553 7573742.76366
|
||||
45 3.32 201383.18845 6359973.47163
|
||||
46 3.325 172173.978278 5355070.91875
|
||||
47 3.33 147548.691578 4520688.28477
|
||||
48 3.335 126734.684289 3825948.80978
|
||||
49 3.34 109098.298235 3245909.11014
|
||||
50 3.345 94118.3261235 2760354.93052
|
||||
51 3.35 81364.827777 2352853.97713
|
||||
52 3.355 70482.1624146 2010008.31682
|
||||
53 3.36 61175.3541703 1720862.26897
|
||||
54 3.365 53199.1018261 1476431.88582
|
||||
55 3.37 46348.8930587 1269329.84244
|
||||
56 3.375 40453.7990113 1093465.44786
|
||||
57 3.38 35370.6146686 943803.998782
|
||||
58 3.385 30979.0803706 816173.162054
|
||||
59 3.39 27177.9744013 707106.743488
|
||||
60 3.395 23881.9094124 613718.268337
|
||||
61 3.4 21018.6991377 533598.403624
|
||||
62 3.405 18527.1884441 464731.50307
|
||||
63 3.41 16355.4608211 405427.532611
|
||||
64 3.415 14459.3541284 354266.400629
|
||||
65 3.42 12801.228731 310052.319542
|
||||
66 3.425 11348.9427887 271776.300627
|
||||
67 3.43 10074.9979765 238585.259865
|
||||
68 3.435 8955.82575185 209756.510836
|
||||
69 3.44 7971.18978782 184676.657916
|
||||
70 3.445 7103.68463562 162824.092297
|
||||
71 3.45 6338.31427303 143754.444665
|
||||
72 3.455 5662.13711315 127088.469763
|
||||
73 3.46 5063.9664184 112501.9356
|
||||
74 3.465 4534.11699728 99717.1686967
|
||||
75 3.47 4064.19064042 88495.970274
|
||||
76 3.475 3646.89404446 78633.6696895
|
||||
77 3.48 3275.88403311 69954.1231906
|
||||
78 3.485 2945.63575657 62305.4999784
|
||||
79 3.49 2651.33026883 55556.7252625
|
||||
80 3.495 2388.75847582 49594.4725913
|
||||
81 3.5 2154.23893796 44320.6162531
|
||||
82 3.505 1944.54741747 39650.0697323
|
||||
83 3.51 1756.8563988 35508.9486835
|
||||
84 3.515 1588.68309151 31833.0071751
|
||||
85 3.52 1437.84465949 28566.3044359
|
||||
86 3.525 1302.41961585 25660.0663588
|
||||
87 3.53 1180.71448694 23071.7118275
|
||||
88 3.535 1071.23498579 20764.0187577
|
||||
89 3.54 972.661050857 18704.4087568
|
||||
90 3.545 883.825202407 16864.3326446
|
||||
91 3.55 803.693750954 15218.7418698
|
||||
92 3.555 731.350460573 13745.6331832
|
||||
93 3.56 665.982328363 12425.6558809
|
||||
94 3.565 606.867190408 11241.7725673
|
||||
95 3.57 553.362906393 10178.9657593
|
||||
96 3.575 504.897910387 9223.98381086
|
||||
97 3.58 460.962945446 8365.12060921
|
||||
98 3.585 421.103825306 7592.02431669
|
||||
99 3.59 384.915088285 6895.53112553
|
||||
100 3.595 352.034427161 6267.5205811
|
||||
101 3.6 322.137794751 5700.78952663
|
||||
102 3.605 294.935098544 5188.94214534
|
||||
103 3.61 270.166409464 4726.29393494
|
||||
104 3.615 247.598619855 4307.78775517
|
||||
105 3.62 227.022494431 3928.92034957
|
||||
106 3.625 208.250065337 3585.67796495
|
||||
107 3.63 191.112328875 3274.47988201
|
||||
108 3.635 175.457206974 2992.12883298
|
||||
109 3.64 161.147741205 2735.76742147
|
||||
110 3.645 148.060491326 2502.83977901
|
||||
111 3.65 136.084113848 2291.05779528
|
||||
112 3.655 125.118099223 2098.37134728
|
||||
113 3.66 115.071648949 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
|
||||
182 4.005 -0.973776490618 6.56057183534
|
||||
183 4.01 -1.00482853285 5.86872847094
|
||||
184 4.015 -1.03254566588 5.22602790624
|
||||
185 4.02 -1.05716510696 4.62911221801
|
||||
186 4.025 -1.07890788015 4.07485905752
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
801 7.1 -0.00331797805604 -0.00620938352214
|
||||
802 7.105 -0.00328703612137 -0.00616744567807
|
||||
803 7.11 -0.00325630304843 -0.00612583832708
|
||||
804 7.115 -0.00322577719224 -0.00608455848864
|
||||
805 7.12 -0.00319545692261 -0.00604360321253
|
||||
806 7.125 -0.00316534062405 -0.00600296957848
|
||||
807 7.13 -0.00313542669558 -0.00596265469582
|
||||
808 7.135 -0.00310571355061 -0.00592265570314
|
||||
809 7.14 -0.00307619961678 -0.005882969768
|
||||
810 7.145 -0.00304688333584 -0.00584359408654
|
||||
811 7.15 -0.00301776316346 -0.00580452588324
|
||||
812 7.155 -0.00298883756913 -0.00576576241051
|
||||
813 7.16 -0.002960105036 -0.00572730094846
|
||||
814 7.165 -0.00293156406078 -0.00568913880453
|
||||
815 7.17 -0.00290321315354 -0.00565127331323
|
||||
816 7.175 -0.00287505083762 -0.0056137018358
|
||||
817 7.18 -0.00284707564951 -0.00557642175992
|
||||
818 7.185 -0.00281928613867 -0.00553943049944
|
||||
819 7.19 -0.00279168086743 -0.00550272549407
|
||||
820 7.195 -0.00276425841086 -0.00546630420907
|
||||
821 7.2 -0.00273701735665 -0.00543016413502
|
||||
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|
||||
823 7.21 -0.00268307386833 -0.00535871770676
|
||||
824 7.215 -0.00265636867152 -0.00532340645761
|
||||
825 7.22 -0.00262983935139 -0.00528836662899
|
||||
826 7.225 -0.00260348455684 -0.00525359583375
|
||||
827 7.23 -0.00257730294861 -0.00521909170842
|
||||
828 7.235 -0.00255129319921 -0.00518485191292
|
||||
829 7.24 -0.00252545399279 -0.00515087413029
|
||||
830 7.245 -0.00249978402504 -0.00511715606646
|
||||
831 7.25 -0.00247428200305 -0.00508369545
|
||||
832 7.255 -0.00244894664521 -0.00505049003185
|
||||
833 7.26 -0.00242377668111 -0.0050175375851
|
||||
834 7.265 -0.00239877085142 -0.00498483590472
|
||||
835 7.27 -0.00237392790776 -0.00495238280735
|
||||
836 7.275 -0.00234924661264 -0.00492017613103
|
||||
837 7.28 -0.00232472573932 -0.004888213735
|
||||
838 7.285 -0.00230036407169 -0.00485649349945
|
||||
839 7.29 -0.00227616040422 -0.00482501332528
|
||||
840 7.295 -0.0022521135418 -0.00479377113392
|
||||
841 7.3 -0.00222822229968 -0.00476276486705
|
||||
842 7.305 -0.00220448550332 -0.00473199248642
|
||||
843 7.31 -0.00218090198837 -0.00470145197362
|
||||
844 7.315 -0.00215747060047 -0.00467114132986
|
||||
845 7.32 -0.00213419019525 -0.00464105857576
|
||||
846 7.325 -0.00211105963817 -0.00461120175114
|
||||
847 7.33 -0.00208807780443 -0.00458156891484
|
||||
848 7.335 -0.00206524357891 -0.00455215814447
|
||||
849 7.34 -0.00204255585605 -0.00452296753622
|
||||
850 7.345 -0.00202001353975 -0.00449399520468
|
||||
851 7.35 -0.00199761554332 -0.00446523928264
|
||||
852 7.355 -0.00197536078933 -0.00443669792087
|
||||
853 7.36 -0.00195324820956 -0.00440836928794
|
||||
854 7.365 -0.00193127674492 -0.00438025157005
|
||||
855 7.37 -0.00190944534533 -0.00435234297081
|
||||
856 7.375 -0.00188775296965 -0.00432464171107
|
||||
857 7.38 -0.00186619858559 -0.00429714602873
|
||||
858 7.385 -0.00184478116965 -0.00426985417856
|
||||
859 7.39 -0.00182349970697 -0.00424276443203
|
||||
860 7.395 -0.00180235319134 -0.00421587507713
|
||||
861 7.4 -0.00178134062504 -0.00418918441815
|
||||
862 7.405 -0.0017604610188 -0.0041626907756
|
||||
863 7.41 -0.0017397133917 -0.00413639248593
|
||||
864 7.415 -0.0017190967711 -0.00411028790146
|
||||
865 7.42 -0.00169861019256 -0.00408437539014
|
||||
866 7.425 -0.00167825269977 -0.00405865333542
|
||||
867 7.43 -0.00165802334445 -0.00403312013606
|
||||
868 7.435 -0.00163792118629 -0.00400777420601
|
||||
869 7.44 -0.00161794529289 -0.00398261397421
|
||||
870 7.445 -0.00159809473965 -0.00395763788446
|
||||
871 7.45 -0.00157836860971 -0.00393284439525
|
||||
872 7.455 -0.00155876599391 -0.00390823197958
|
||||
873 7.46 -0.00153928599065 -0.00388379912488
|
||||
874 7.465 -0.00151992770589 -0.00385954433278
|
||||
875 7.47 -0.00150069025303 -0.00383546611901
|
||||
876 7.475 -0.00148157275285 -0.00381156301323
|
||||
877 7.48 -0.00146257433348 -0.0037878335589
|
||||
878 7.485 -0.00144369413025 -0.00376427631313
|
||||
879 7.49 -0.00142493128571 -0.00374088984652
|
||||
880 7.495 -0.00140628494952 -0.00371767274304
|
||||
881 7.5 -0.00138775427835 -0.00369462359991
|
||||
882 7.505 -0.0013693384359 -0.00367174102741
|
||||
883 7.51 -0.00135103659275 -0.00364902364878
|
||||
884 7.515 -0.00133284792636 -0.00362647010008
|
||||
885 7.52 -0.00131477162096 -0.00360407903007
|
||||
886 7.525 -0.0012968068675 -0.00358184910005
|
||||
887 7.53 -0.0012789528636 -0.00355977898374
|
||||
888 7.535 -0.00126120881349 -0.00353786736716
|
||||
889 7.54 -0.00124357392793 -0.00351611294851
|
||||
890 7.545 -0.00122604742416 -0.00349451443802
|
||||
891 7.55 -0.00120862852584 -0.00347307055786
|
||||
892 7.555 -0.00119131646298 -0.00345178004197
|
||||
893 7.56 -0.0011741104719 -0.00343064163599
|
||||
894 7.565 -0.00115700979517 -0.0034096540971
|
||||
895 7.57 -0.00114001368154 -0.00338881619393
|
||||
896 7.575 -0.00112312138587 -0.00336812670643
|
||||
897 7.58 -0.00110633216913 -0.00334758442575
|
||||
898 7.585 -0.00108964529827 -0.00332718815413
|
||||
899 7.59 -0.00107306004622 -0.00330693670479
|
||||
900 7.595 -0.00105657569181 -0.00328682890181
|
||||
901 7.6 -0.00104019151973 -0.00326686358005
|
||||
902 7.605 -0.00102390682047 -0.00324703958498
|
||||
903 7.61 -0.00100772089024 -0.00322735577263
|
||||
904 7.615 -0.000991633030992 -0.00320781100945
|
||||
905 7.62 -0.000975642550274 -0.00318840417222
|
||||
906 7.625 -0.000959748761248 -0.00316913414793
|
||||
907 7.63 -0.000943950982612 -0.00314999983371
|
||||
908 7.635 -0.00092824853855 -0.00313100013668
|
||||
909 7.64 -0.000912640758688 -0.00311213397388
|
||||
910 7.645 -0.000897126978043 -0.00309340027216
|
||||
911 7.65 -0.000881706536971 -0.0030747979681
|
||||
912 7.655 -0.000866378781123 -0.00305632600787
|
||||
913 7.66 -0.000851143061394 -0.00303798334719
|
||||
914 7.665 -0.000835998733877 -0.00301976895117
|
||||
915 7.67 -0.000820945159817 -0.00300168179428
|
||||
916 7.675 -0.000805981705564 -0.0029837208602
|
||||
917 7.68 -0.000791107742523 -0.00296588514177
|
||||
918 7.685 -0.000776322647117 -0.00294817364088
|
||||
919 7.69 -0.000761625800734 -0.00293058536838
|
||||
920 7.695 -0.000747016589687 -0.00291311934398
|
||||
921 7.7 -0.000732494405167 -0.00289577459618
|
||||
922 7.705 -0.000718058643203 -0.00287855016219
|
||||
923 7.71 -0.000703708704613 -0.0028614450878
|
||||
924 7.715 -0.000689443994968 -0.00284445842736
|
||||
925 7.72 -0.000675263924546 -0.00282758924361
|
||||
926 7.725 -0.000661167908286 -0.0028108366077
|
||||
927 7.73 -0.000647155365757 -0.002794199599
|
||||
928 7.735 -0.000633225721105 -0.00277767730511
|
||||
929 7.74 -0.000619378403022 -0.00276126882172
|
||||
930 7.745 -0.000605612844698 -0.00274497325255
|
||||
931 7.75 -0.000591928483787 -0.00272878970927
|
||||
932 7.755 -0.000578324762364 -0.00271271731143
|
||||
933 7.76 -0.000564801126885 -0.00269675518635
|
||||
934 7.765 -0.000551357028154 -0.00268090246909
|
||||
935 7.77 -0.000537991921277 -0.00266515830234
|
||||
936 7.775 -0.00052470526563 -0.00264952183636
|
||||
937 7.78 -0.000511496524817 -0.00263399222891
|
||||
938 7.785 -0.000498365166635 -0.00261856864514
|
||||
939 7.79 -0.000485310663039 -0.00260325025757
|
||||
940 7.795 -0.0004723324901 -0.00258803624599
|
||||
941 7.8 -0.000459430127974 -0.00257292579737
|
||||
942 7.805 -0.000446603060865 -0.00255791810586
|
||||
943 7.81 -0.000433850776986 -0.00254301237261
|
||||
944 7.815 -0.000421172768528 -0.00252820780582
|
||||
945 7.82 -0.000408568531625 -0.00251350362058
|
||||
946 7.825 -0.000396037566317 -0.00249889903884
|
||||
947 7.83 -0.000383579376517 -0.00248439328937
|
||||
948 7.835 -0.000371193469977 -0.00246998560763
|
||||
949 7.84 -0.000358879358258 -0.00245567523575
|
||||
950 7.845 -0.000346636556689 -0.00244146142247
|
||||
951 7.85 -0.000334464584344 -0.00242734342306
|
||||
952 7.855 -0.000322362964 -0.00241332049923
|
||||
953 7.86 -0.000310331222112 -0.00239939191913
|
||||
954 7.865 -0.000298368888779 -0.00238555695723
|
||||
955 7.87 -0.000286475497709 -0.00237181489431
|
||||
956 7.875 -0.000274650586192 -0.00235816501734
|
||||
957 7.88 -0.00026289369507 -0.00234460661948
|
||||
958 7.885 -0.000251204368701 -0.00233113899997
|
||||
959 7.89 -0.000239582154932 -0.00231776146411
|
||||
960 7.895 -0.000228026605069 -0.00230447332318
|
||||
961 7.9 -0.000216537273846 -0.0022912738944
|
||||
962 7.905 -0.000205113719399 -0.00227816250086
|
||||
963 7.91 -0.000193755503231 -0.00226513847144
|
||||
964 7.915 -0.000182462190187 -0.00225220114081
|
||||
965 7.92 -0.000171233348425 -0.00223934984935
|
||||
966 7.925 -0.000160068549386 -0.00222658394306
|
||||
967 7.93 -0.000148967367767 -0.00221390277357
|
||||
968 7.935 -0.000137929381494 -0.00220130569803
|
||||
969 7.94 -0.000126954171692 -0.00218879207909
|
||||
970 7.945 -0.000116041322662 -0.00217636128485
|
||||
971 7.95 -0.000105190421847 -0.00216401268878
|
||||
972 7.955 -9.44010598127e-05 -0.00215174566969
|
||||
973 7.96 -8.36728302154e-05 -0.0021395596117
|
||||
974 7.965 -7.30053297786e-05 -0.00212745390412
|
||||
975 7.97 -6.23981582662e-05 -0.00211542794149
|
||||
976 7.975 -5.18509184563e-05 -0.00210348112347
|
||||
977 7.98 -4.13632161162e-05 -0.0020916128548
|
||||
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
|
||||
|
|
@ -0,0 +1,989 @@
|
|||
# Interaction between a chaperone wall and hydrophilic ("L", "N") beads (h=0.0)
|
||||
# Generated using:
|
||||
# generate_tables/calc_chaperone_table.py 1.0 1.0 3.0 0.00 3.1 8.0 981 True
|
||||
|
||||
CH_H0
|
||||
N 981 R 3.1 8.0
|
||||
|
||||
1 3.1 24322007640.7 2.44004657299e+12
|
||||
2 3.105 14907558394.3 1.42456861215e+12
|
||||
3 3.11 9347035105.18 8.52735941633e+11
|
||||
4 3.115 5983077933.86 5.22188377701e+11
|
||||
5 3.12 3902959636.31 3.26497584961e+11
|
||||
6 3.125 2590663239.27 2.08082071378e+11
|
||||
7 3.13 1747363476.38 1.34970838198e+11
|
||||
8 3.135 1196150660.14 88985299862.7
|
||||
9 3.14 830139558.184 59560058382.9
|
||||
10 3.145 583526310.01 40428734750.9
|
||||
11 3.15 415085889.414 27804165925.8
|
||||
12 3.155 298569038.21 19357152203.7
|
||||
13 3.16 217007230.904 13631625105.8
|
||||
14 3.165 159275126.218 9703361847.17
|
||||
15 3.17 117981153.625 6977285889.84
|
||||
16 3.175 88152959.6539 5065076691.93
|
||||
17 3.18 66406248.0614 3710118471.36
|
||||
18 3.185 50412054.1061 2740803858.1
|
||||
19 3.19 38550891.1571 2041079190.29
|
||||
20 3.195 29685484.2812 1531623758.63
|
||||
21 3.2 23009711.8183 1157676125.86
|
||||
22 3.205 17947107.7408 881068391.885
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|
||||
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
|
||||
|
||||
|
|
@ -0,0 +1,24 @@
|
|||
# -- Init section --
|
||||
|
||||
include system.in.init
|
||||
|
||||
# -- Atom definition section --
|
||||
|
||||
read_data system.data
|
||||
|
||||
# -- Settings Section --
|
||||
|
||||
include system.in.settings
|
||||
|
||||
# Optional: Make sure the pairwise energies look reasonable:
|
||||
pair_write 1 4 1001 r 4.05 8 test_chap-B.dat C-B 0 0
|
||||
pair_write 2 4 1001 r 4.05 8 test_chap-L.dat C-L 0 0
|
||||
pair_write 3 4 1001 r 4.05 8 test_chap-N.dat C-N 0 0
|
||||
|
||||
# -- Run section --
|
||||
|
||||
dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz
|
||||
|
||||
minimize 1.0e-5 1.0e-7 500 2000
|
||||
|
||||
write_restart system_after_min.rst
|
||||
|
|
@ -0,0 +1,46 @@
|
|||
# -- Init Section --
|
||||
|
||||
include system.in.init
|
||||
|
||||
# -- Atom Definition Section --
|
||||
|
||||
# I you want to be careful, you can minimize the system first. (Try using
|
||||
# "run.in.min" and uncomment the read_restart command in this file below.)
|
||||
# read_restart system_after_min.rst
|
||||
|
||||
read_data system.data
|
||||
|
||||
# -- Settings Section --
|
||||
|
||||
include system.in.settings
|
||||
|
||||
# -- Run Section --
|
||||
|
||||
|
||||
timestep 0.025
|
||||
dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz
|
||||
|
||||
# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve".
|
||||
# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.)
|
||||
|
||||
fix fxlan all langevin 0.25 0.25 1.0 48279
|
||||
fix fxnve all nve
|
||||
|
||||
# Notes:
|
||||
# The temperature is in reduced units and is set to 0.25
|
||||
# which is the folding temperature for the frustrated protein
|
||||
# The inverse-damping-rate "damp" (which has units of time) is set to 1.0,
|
||||
# as it was in the paper. (Hopefully folding times should be similar.)
|
||||
# (See http://lammps.sandia.gov/doc/fix_langevin.html)
|
||||
|
||||
|
||||
thermo_style custom step temp pe etotal press vol epair ebond eangle edihed
|
||||
thermo_modify norm no #(report total energy not energy / num_atoms)
|
||||
thermo 5000 #(time interval for printing out "thermo" data)
|
||||
|
||||
#restart 100000000 restart_nvt
|
||||
|
||||
run 1000000000
|
||||
|
||||
write_restart system_after_nvt.rst
|
||||
|
||||
|
|
@ -0,0 +1,29 @@
|
|||
# This directory demonstrates how to run a short simulation of
|
||||
# the "frustrated" coarse-grained protein model used in:
|
||||
# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
|
||||
# (http://www.pnas.org/content/101/36/13192)
|
||||
#
|
||||
# During this short simulation (run_short_sim.nvt.in) the protein evolves
|
||||
# from an unfolded initial conformation to a misfolded conformation.
|
||||
# (Visualize using VMD. Note: It can take hundreds of millions of
|
||||
# timesteps to escape from this conformation and reach the folded state.)
|
||||
#
|
||||
# -------- REQUIREMENTS: ---------
|
||||
# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC")
|
||||
# http://lammps.sandia.gov/doc/Section_start.html#start_3
|
||||
# 2) It also may require additional features and bug fixes for LAMMPS.
|
||||
# be sure to download and copy the "additional_lammps_code" from
|
||||
# http://moltemplate.org (upper-left corner menu)
|
||||
# 3) Unpack it
|
||||
# 4) copy the .cpp and .h files to the src folding of your lammps installation.
|
||||
# 5) Compile LAMMPS.
|
||||
|
||||
-------------
|
||||
Instructions on how to build LAMMPS input files and
|
||||
run a short simulation are provided in other README files.
|
||||
|
||||
step 1)
|
||||
README_setup.sh
|
||||
|
||||
step2)
|
||||
README_run.sh
|
||||
|
|
@ -0,0 +1,21 @@
|
|||
# You would probably run lammps this way:
|
||||
#
|
||||
# lmp_ubuntu -i run.in.nvt
|
||||
|
||||
# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer
|
||||
# to the input scripts & data files you created earlier when you ran moltemplate
|
||||
# system.in.init, system.in.settings, system.data
|
||||
|
||||
|
||||
# -----------------------------------
|
||||
|
||||
LAMMPS_COMMAND="lmp_ubuntu"
|
||||
|
||||
# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps
|
||||
# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary.
|
||||
|
||||
# Run lammps using the following 3 commands:
|
||||
|
||||
"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL)
|
||||
"$LAMMPS_COMMAND" -i run_short_sim.in.nvt # production run
|
||||
|
||||
|
|
@ -0,0 +1,24 @@
|
|||
# Use these commands to generate the LAMMPS input script and data file
|
||||
# (and other auxilliary files):
|
||||
|
||||
|
||||
# Create LAMMPS input files this way:
|
||||
cd moltemplate_files
|
||||
|
||||
# run moltemplate
|
||||
|
||||
moltemplate.sh -overlay-dihdedrals system.lt
|
||||
|
||||
# This will generate various files with names ending in *.in* and *.data.
|
||||
# These files are the input files directly read by LAMMPS. Move them to
|
||||
# the parent directory (or wherever you plan to run the simulation).
|
||||
|
||||
mv -f system.in* system.data ../
|
||||
cp -r table*.dat ../
|
||||
|
||||
# Optional:
|
||||
# The "./output_ttree/" directory is full of temporary files generated by
|
||||
# moltemplate. They can be useful for debugging, but are usually thrown away.
|
||||
rm -rf output_ttree/
|
||||
|
||||
cd ../
|
||||
|
|
@ -0,0 +1,87 @@
|
|||
|
||||
------- To view a lammps trajectory in VMD --------
|
||||
|
||||
|
||||
1) Build a PSF file for use in viewing with VMD.
|
||||
|
||||
This step works with VMD 1.9 and topotools 1.2.
|
||||
(Older versions, like VMD 1.8.6, don't support this.)
|
||||
|
||||
|
||||
a) Start VMD
|
||||
b) Menu Extensions->Tk Console
|
||||
c) Enter:
|
||||
|
||||
(I assume that the the DATA file is called "system.data")
|
||||
|
||||
topo readlammpsdata system.data full
|
||||
animate write psf system.psf
|
||||
|
||||
2)
|
||||
|
||||
Later, to Load a trajectory in VMD:
|
||||
|
||||
Start VMD
|
||||
Select menu: File->New Molecule
|
||||
-Browse to select the PSF file you created above, and load it.
|
||||
(Don't close the window yet.)
|
||||
-Browse to select the trajectory file.
|
||||
If necessary, for "file type" select: "LAMMPS Trajectory"
|
||||
Load it.
|
||||
|
||||
---- A note on trajectory format: -----
|
||||
If the trajectory is a DUMP file, then make sure the it contains the
|
||||
information you need for pbctools (see below. I've been using this
|
||||
command in my LAMMPS scripts to create the trajectories:
|
||||
|
||||
dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
|
||||
|
||||
It's a good idea to use an atom_style which supports molecule-ID numbers
|
||||
so that you can assign a molecule-ID number to each atom. (I think this
|
||||
is needed to wrap atom coordinates without breaking molecules in half.)
|
||||
|
||||
Of course, you don't have to save your trajectories in DUMP format,
|
||||
(other formats like DCD work fine) I just mention dump files
|
||||
because these are the files I'm familiar with.
|
||||
|
||||
3) ----- Wrap the coordinates to the unit cell
|
||||
(without cutting the molecules in half)
|
||||
|
||||
a) Start VMD
|
||||
b) Load the trajectory in VMD (see above)
|
||||
c) Menu Extensions->Tk Console
|
||||
d) Try entering these commands:
|
||||
|
||||
pbc wrap -compound res -all
|
||||
pbc box
|
||||
|
||||
----- Optional ----
|
||||
Sometimes the solvent or membrane obscures the view of the solute.
|
||||
It can help to shift the location of the periodic boundary box
|
||||
To shift the box in the y direction (for example) do this:
|
||||
|
||||
pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
|
||||
pbc box -shiftcenterrel {0.0 0.15 0.0}
|
||||
|
||||
Distances are measured in units of box-length fractions, not Angstroms.
|
||||
|
||||
Alternately if you have a solute whose atoms are all of type 1,
|
||||
then you can also try this to center the box around it:
|
||||
|
||||
pbc wrap -sel type=1 -all -centersel type=2 -center com
|
||||
|
||||
4)
|
||||
You should check if your periodic boundary conditions are too small.
|
||||
To do that:
|
||||
select Graphics->Representations menu option
|
||||
click on the "Periodic" tab, and
|
||||
click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
|
||||
|
||||
5) Optional: If you like, change the atom types in the PSF file so
|
||||
that VMD recognizes the atom types, use something like:
|
||||
|
||||
sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
|
||||
sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
|
||||
sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
|
||||
|
||||
(If you do this, it might effect step 2 above.)
|
||||
|
|
@ -0,0 +1,85 @@
|
|||
PSF
|
||||
|
||||
1 !NTITLE
|
||||
REMARKS VMD generated structure x-plor psf file
|
||||
|
||||
27 !NATOM
|
||||
1 1 2 2 0.000000 1.0000 0
|
||||
2 1 1 1 0.000000 1.0000 0
|
||||
3 1 2 2 0.000000 1.0000 0
|
||||
4 1 1 1 0.000000 1.0000 0
|
||||
5 1 2 2 0.000000 1.0000 0
|
||||
6 1 1 1 0.000000 1.0000 0
|
||||
7 1 3 3 0.000000 1.0000 0
|
||||
8 1 3 3 0.000000 1.0000 0
|
||||
9 1 1 1 0.000000 1.0000 0
|
||||
10 1 2 2 0.000000 1.0000 0
|
||||
11 1 1 1 0.000000 1.0000 0
|
||||
12 1 2 2 0.000000 1.0000 0
|
||||
13 1 1 1 0.000000 1.0000 0
|
||||
14 1 2 2 0.000000 1.0000 0
|
||||
15 1 3 3 0.000000 1.0000 0
|
||||
16 1 3 3 0.000000 1.0000 0
|
||||
17 1 3 3 0.000000 1.0000 0
|
||||
18 1 1 1 0.000000 1.0000 0
|
||||
19 1 1 1 0.000000 1.0000 0
|
||||
20 1 2 2 0.000000 1.0000 0
|
||||
21 1 2 2 0.000000 1.0000 0
|
||||
22 1 1 1 0.000000 1.0000 0
|
||||
23 1 1 1 0.000000 1.0000 0
|
||||
24 1 2 2 0.000000 1.0000 0
|
||||
25 1 2 2 0.000000 1.0000 0
|
||||
26 1 1 1 0.000000 1.0000 0
|
||||
27 1 2 2 0.000000 1.0000 0
|
||||
|
||||
26 !NBOND: bonds
|
||||
1 2 2 3 3 4 4 5
|
||||
5 6 6 7 7 8 8 9
|
||||
9 10 10 11 11 12 12 13
|
||||
13 14 14 15 15 16 16 17
|
||||
17 18 18 19 19 20 20 21
|
||||
21 22 22 23 23 24 24 25
|
||||
25 26 26 27
|
||||
|
||||
25 !NTHETA: angles
|
||||
13 14 15 7 8 9 6 7 8
|
||||
16 17 18 15 16 17 2 3 4
|
||||
4 5 6 9 10 11 11 12 13
|
||||
14 15 16 1 2 3 3 4 5
|
||||
10 11 12 12 13 14 25 26 27
|
||||
5 6 7 8 9 10 17 18 19
|
||||
18 19 20 22 23 24 21 22 23
|
||||
19 20 21 20 21 22 23 24 25
|
||||
24 25 26
|
||||
|
||||
19 !NPHI: dihedrals
|
||||
1 2 3 4 2 3 4 5
|
||||
3 4 5 6 4 5 6 7
|
||||
8 9 10 11 9 10 11 12
|
||||
10 11 12 13 11 12 13 14
|
||||
12 13 14 15 15 16 17 18
|
||||
16 17 18 19 17 18 19 20
|
||||
18 19 20 21 19 20 21 22
|
||||
20 21 22 23 21 22 23 24
|
||||
22 23 24 25 23 24 25 26
|
||||
24 25 26 27
|
||||
|
||||
0 !NIMPHI: impropers
|
||||
|
||||
|
||||
0 !NDON: donors
|
||||
|
||||
|
||||
0 !NACC: acceptors
|
||||
|
||||
|
||||
0 !NNB
|
||||
|
||||
0 0 0 0 0 0 0 0
|
||||
0 0 0 0 0 0 0 0
|
||||
0 0 0 0 0 0 0 0
|
||||
0 0 0
|
||||
|
||||
1 0 !NGRP
|
||||
0 0 0
|
||||
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 23 KiB |
Binary file not shown.
|
After Width: | Height: | Size: 22 KiB |
|
|
@ -0,0 +1,216 @@
|
|||
# This file defines the "frustrated" coarse-grained protein model used in:
|
||||
# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
|
||||
# (http://www.pnas.org/content/101/36/13192)
|
||||
|
||||
|
||||
1beadFrustrated {
|
||||
|
||||
# There are 3 atom types (referred to above as B, L, and N)
|
||||
# Define their masses:
|
||||
|
||||
write_once("Data Masses") {
|
||||
@atom:B 1.0
|
||||
@atom:L 1.0
|
||||
@atom:N 1.0
|
||||
}
|
||||
|
||||
# AtomID MoleculeID AtomType Charge X Y Z
|
||||
|
||||
write("Data Atoms") {
|
||||
$atom:a1 $mol @atom:L 0.0 -0.92636654 -1.8409904 -2.1482679
|
||||
$atom:a2 $mol @atom:B 0.0 -0.57313354 -1.0670787 -1.6182341
|
||||
$atom:a3 $mol @atom:L 0.0 -0.85707399 -1.2358703 -0.69350966
|
||||
$atom:a4 $mol @atom:B 0.0 -0.44231274 -0.4584993 -0.23418709
|
||||
$atom:a5 $mol @atom:L 0.0 -0.75081182 -0.62868078 0.69786737
|
||||
$atom:a6 $mol @atom:B 0.0 -0.36201977 0.11619615 1.2249098
|
||||
$atom:a7 $mol @atom:N 0.0 -0.63708237 -0.15973084 2.1723919
|
||||
$atom:a8 $mol @atom:N 0.0 0.20516047 0.10417157 2.624901
|
||||
$atom:a9 $mol @atom:B 0.0 0.57223743 0.44728103 1.7695617
|
||||
$atom:a10 $mol @atom:L 0.0 0.77646279 -0.40630393 1.3168043
|
||||
$atom:a11 $mol @atom:B 0.0 0.45475664 -0.2077937 0.40045721
|
||||
$atom:a12 $mol @atom:L 0.0 0.72712495 -1.0397637 -0.087614951
|
||||
$atom:a13 $mol @atom:B 0.0 0.36971183 -0.85840501 -0.9933019
|
||||
$atom:a14 $mol @atom:L 0.0 0.74784336 -1.5700415 -1.5859217
|
||||
$atom:a15 $mol @atom:N 0.0 0.43423905 -1.2758917 -2.4853429
|
||||
$atom:a16 $mol @atom:N 0.0 0.70583191 -0.30726921 -2.4987711
|
||||
$atom:a17 $mol @atom:N 0.0 -0.091688915 0.23323014 -2.2051358
|
||||
$atom:a18 $mol @atom:B 0.0 -0.34243283 -0.035822049 -1.2644719
|
||||
$atom:a19 $mol @atom:B 0.0 0.41961247 0.18475451 -0.65971014
|
||||
$atom:a20 $mol @atom:L 0.0 0.51968465 1.1546791 -0.77877053
|
||||
$atom:a21 $mol @atom:L 0.0 -0.40827985 1.2765273 -0.52550748
|
||||
$atom:a22 $mol @atom:B 0.0 -0.368141 0.58090904 0.19152224
|
||||
$atom:a23 $mol @atom:B 0.0 0.40327249 0.86101769 0.7336255
|
||||
$atom:a24 $mol @atom:L 0.0 0.22707289 1.8326235 0.89673346
|
||||
$atom:a25 $mol @atom:L 0.0 -0.66500182 1.7285809 1.2783166
|
||||
$atom:a26 $mol @atom:B 0.0 -0.39205603 1.0475436 1.9328097
|
||||
$atom:a27 $mol @atom:L 0.0 0.25339027 1.5246265 2.5388463
|
||||
}
|
||||
|
||||
# bond-ID bond-Type atom-ID atom-ID
|
||||
|
||||
write("Data Bonds") {
|
||||
$bond:b1 @bond:backbone $atom:a1 $atom:a2
|
||||
$bond:b2 @bond:backbone $atom:a2 $atom:a3
|
||||
$bond:b3 @bond:backbone $atom:a3 $atom:a4
|
||||
$bond:b4 @bond:backbone $atom:a4 $atom:a5
|
||||
$bond:b5 @bond:backbone $atom:a5 $atom:a6
|
||||
$bond:b6 @bond:backbone $atom:a6 $atom:a7
|
||||
$bond:b7 @bond:backbone $atom:a7 $atom:a8
|
||||
$bond:b8 @bond:backbone $atom:a8 $atom:a9
|
||||
$bond:b9 @bond:backbone $atom:a9 $atom:a10
|
||||
$bond:b10 @bond:backbone $atom:a10 $atom:a11
|
||||
$bond:b11 @bond:backbone $atom:a11 $atom:a12
|
||||
$bond:b12 @bond:backbone $atom:a12 $atom:a13
|
||||
$bond:b13 @bond:backbone $atom:a13 $atom:a14
|
||||
$bond:b14 @bond:backbone $atom:a14 $atom:a15
|
||||
$bond:b15 @bond:backbone $atom:a15 $atom:a16
|
||||
$bond:b16 @bond:backbone $atom:a16 $atom:a17
|
||||
$bond:b17 @bond:backbone $atom:a17 $atom:a18
|
||||
$bond:b18 @bond:backbone $atom:a18 $atom:a19
|
||||
$bond:b19 @bond:backbone $atom:a19 $atom:a20
|
||||
$bond:b20 @bond:backbone $atom:a20 $atom:a21
|
||||
$bond:b21 @bond:backbone $atom:a21 $atom:a22
|
||||
$bond:b22 @bond:backbone $atom:a22 $atom:a23
|
||||
$bond:b23 @bond:backbone $atom:a23 $atom:a24
|
||||
$bond:b24 @bond:backbone $atom:a24 $atom:a25
|
||||
$bond:b25 @bond:backbone $atom:a25 $atom:a26
|
||||
$bond:b26 @bond:backbone $atom:a26 $atom:a27
|
||||
}
|
||||
|
||||
# (3-body) Angles are specified below
|
||||
|
||||
# (4-body) Dihedrals must be defined explicitly for every quartet of atoms.
|
||||
# (These interactions are not determined by atom type.)
|
||||
|
||||
# dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID
|
||||
|
||||
write("Data Dihedrals") {
|
||||
|
||||
$dihedral:d1 @dihedral:beta $atom:a1 $atom:a2 $atom:a3 $atom:a4
|
||||
$dihedral:d2 @dihedral:beta $atom:a2 $atom:a3 $atom:a4 $atom:a5
|
||||
$dihedral:d3 @dihedral:beta $atom:a3 $atom:a4 $atom:a5 $atom:a6
|
||||
$dihedral:d4 @dihedral:beta $atom:a4 $atom:a5 $atom:a6 $atom:a7
|
||||
|
||||
# Dihedral angle forces in the turn regions were switched off
|
||||
# (in this model) so just I comment them out (and \ the variable names).
|
||||
# \$dihedral:d5 \@dihedral:turn $atom:a5 $atom:a6 $atom:a7 $atom:a8
|
||||
# \$dihedral:d6 \@dihedral:turn $atom:a6 $atom:a7 $atom:a8 $atom:a9
|
||||
# \$dihedral:d7 \@dihedral:turn $atom:a7 $atom:a8 $atom:a9 $atom:a10
|
||||
|
||||
$dihedral:d8 @dihedral:beta $atom:a8 $atom:a9 $atom:a10 $atom:a11
|
||||
$dihedral:d9 @dihedral:beta $atom:a9 $atom:a10 $atom:a11 $atom:a12
|
||||
$dihedral:d10 @dihedral:beta $atom:a10 $atom:a11 $atom:a12 $atom:a13
|
||||
$dihedral:d11 @dihedral:beta $atom:a11 $atom:a12 $atom:a13 $atom:a14
|
||||
$dihedral:d12 @dihedral:beta $atom:a12 $atom:a13 $atom:a14 $atom:a15
|
||||
|
||||
# Dihedral angle forces in the turn regions were switched off
|
||||
# (in this model) so just I comment them out (and \ the variable names).
|
||||
# \$dihedral:d13 \@dihedral:turn $atom:a13 $atom:a14 $atom:a15 $atom:a16
|
||||
# \$dihedral:d14 \@dihedral:turn $atom:a14 $atom:a15 $atom:a16 $atom:a17
|
||||
|
||||
$dihedral:d15 @dihedral:alpha $atom:a15 $atom:a16 $atom:a17 $atom:a18
|
||||
$dihedral:d16 @dihedral:alpha $atom:a16 $atom:a17 $atom:a18 $atom:a19
|
||||
$dihedral:d17 @dihedral:alpha $atom:a17 $atom:a18 $atom:a19 $atom:a20
|
||||
$dihedral:d18 @dihedral:alpha $atom:a18 $atom:a19 $atom:a20 $atom:a21
|
||||
$dihedral:d19 @dihedral:alpha $atom:a19 $atom:a20 $atom:a21 $atom:a22
|
||||
$dihedral:d20 @dihedral:alpha $atom:a20 $atom:a21 $atom:a22 $atom:a23
|
||||
$dihedral:d21 @dihedral:alpha $atom:a21 $atom:a22 $atom:a23 $atom:a24
|
||||
$dihedral:d22 @dihedral:alpha $atom:a22 $atom:a23 $atom:a24 $atom:a25
|
||||
$dihedral:d23 @dihedral:alpha $atom:a23 $atom:a24 $atom:a25 $atom:a26
|
||||
$dihedral:d24 @dihedral:alpha $atom:a24 $atom:a25 $atom:a26 $atom:a27
|
||||
}
|
||||
|
||||
# All consecutively bonded triplets of atoms same 3-body bond-angle
|
||||
# interaction parameters. Of coarse, we could specify them all explicitly
|
||||
# (as we did for the dihedrals above), but I wanted to show how to specify
|
||||
# angles by atom type instead. (You can do this for dihedrals & impropers
|
||||
# also.)
|
||||
|
||||
# angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type
|
||||
|
||||
write_once("Data Angles By Type") {
|
||||
@angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:*
|
||||
}
|
||||
|
||||
# (The "*" is a wildcard character. I use "*" to denote any atom-type or
|
||||
# bond-type which is defined within the current namespace: 1beadFrustrated)
|
||||
|
||||
|
||||
# 2-body (non-bonded) interactions:
|
||||
#
|
||||
# Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6)
|
||||
#
|
||||
# i j pairstylename eps sig K L
|
||||
#
|
||||
write_once("In Settings") {
|
||||
pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1
|
||||
pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0
|
||||
pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0
|
||||
pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1
|
||||
pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0
|
||||
pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0
|
||||
}
|
||||
|
||||
|
||||
# 2-body (bonded) interactions:
|
||||
#
|
||||
# Ubond(r) = (k/2)*(r-0)^2
|
||||
#
|
||||
# The corresponding command is:
|
||||
#
|
||||
# bond-Type bondstylename k r0
|
||||
|
||||
write_once("In Settings") {
|
||||
bond_coeff @bond:backbone harmonic 100.0 1.0
|
||||
}
|
||||
|
||||
# 3-body interactions in this example are listed by atomType and bondType
|
||||
# The atomIDs involved are determined automatically. The forumula used is:
|
||||
#
|
||||
# Uangle(theta) = (k/2)*(theta-theta0)^2
|
||||
# (k in kcal/mol/rad^2, theta0 in degrees)
|
||||
#
|
||||
# angle-Type anglestylename k theta0
|
||||
|
||||
write_once("In Settings") {
|
||||
angle_coeff @angle:backbone harmonic 13.3333333333 105.0
|
||||
}
|
||||
|
||||
|
||||
# We use tabular dihedral potentials to implement the dihedral forces.
|
||||
# (Actually there is a way to use Fourier series, using multiple charmm
|
||||
# style dihedral interactions, but it's slower and messier.)
|
||||
|
||||
write_once("In Settings") {
|
||||
# style file keyword
|
||||
dihedral_coeff @dihedral:alpha table table_dihedral_frustrated.dat FRUSTRATED_ALPHA
|
||||
dihedral_coeff @dihedral:beta table table_dihedral_frustrated.dat FRUSTRATED_BETA
|
||||
# No need to specify dihedral interactions in the turn regions. (none exist)
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
# Optional: define the atoms in the "proteins" group
|
||||
group proteins type @atom:B
|
||||
group proteins type @atom:L
|
||||
group proteins type @atom:N
|
||||
}
|
||||
|
||||
# LAMMPS has many available force field styles (and atom styles).
|
||||
# Here, we pick the ones which work well for this molecular model:
|
||||
|
||||
write_once("In Init") {
|
||||
# --- Default options for the "1BeadFrustrated" protein model ---
|
||||
# --- (These can be overridden later.) ---
|
||||
units lj
|
||||
atom_style full
|
||||
bond_style hybrid harmonic
|
||||
angle_style hybrid harmonic
|
||||
dihedral_style hybrid table spline 360
|
||||
pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0
|
||||
pair_modify mix arithmetic
|
||||
special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions)
|
||||
}
|
||||
|
||||
} # 1beadFrustrated
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,85 @@
|
|||
import "1beadFrustrated.lt"
|
||||
|
||||
|
||||
# Alternate starting conformation (same molecule):
|
||||
|
||||
|
||||
1beadMisfolded inherits 1beadFrustrated {
|
||||
|
||||
# This molecule "inherits" all of its features from "1beadFrustrated".
|
||||
# Here we override the atomic positions with new coordinates:
|
||||
|
||||
# AtomID MoleculeID AtomType Charge X Y Z
|
||||
|
||||
write("Data Atoms") {
|
||||
$atom:a1 $mol @atom:L 0.0 -0.69801399 -0.22114168 -1.9464876
|
||||
$atom:a2 $mol @atom:B 0.0 -0.40921658 -0.027063664 -1.0033251
|
||||
$atom:a3 $mol @atom:L 0.0 0.10259348 0.80836418 -1.0737085
|
||||
$atom:a4 $mol @atom:B 0.0 0.25857916 1.0054984 -0.11621451
|
||||
$atom:a5 $mol @atom:L 0.0 0.8258629 1.8325549 -0.18529135
|
||||
$atom:a6 $mol @atom:B 0.0 0.91366257 2.1950317 0.74175977
|
||||
$atom:a7 $mol @atom:N 0.0 1.4399539 1.554238 1.2994409
|
||||
$atom:a8 $mol @atom:N 0.0 0.73372573 1.0161012 1.7397275
|
||||
$atom:a9 $mol @atom:B 0.0 0.26608782 0.65302497 0.94353938
|
||||
$atom:a10 $mol @atom:L 0.0 0.97442305 0.13574211 0.50586398
|
||||
$atom:a11 $mol @atom:B 0.0 0.35889617 -0.18247555 -0.1764186
|
||||
$atom:a12 $mol @atom:L 0.0 0.87151735 -0.77260824 -0.75240916
|
||||
$atom:a13 $mol @atom:B 0.0 0.047726486 -1.0530682 -1.1902704
|
||||
$atom:a14 $mol @atom:L 0.0 0.34530697 -1.7476773 -1.8393331
|
||||
$atom:a15 $mol @atom:N 0.0 0.65865186 -2.45948 -1.2167056
|
||||
$atom:a16 $mol @atom:N 0.0 -0.16534524 -2.6219442 -0.67112167
|
||||
$atom:a17 $mol @atom:N 0.0 -0.010590421 -2.2445242 0.24748633
|
||||
$atom:a18 $mol @atom:B 0.0 0.18135771 -1.2564919 0.1767523
|
||||
$atom:a19 $mol @atom:B 0.0 -0.57472665 -0.82852797 -0.27027791
|
||||
$atom:a20 $mol @atom:L 0.0 -1.3967448 -1.0516787 0.24247346
|
||||
$atom:a21 $mol @atom:L 0.0 -1.003428 -0.85642681 1.1107555
|
||||
$atom:a22 $mol @atom:B 0.0 -0.25156735 -0.3182346 0.74262946
|
||||
$atom:a23 $mol @atom:B 0.0 -0.61751956 0.30115562 0.070426493
|
||||
$atom:a24 $mol @atom:L 0.0 -1.3347934 0.83310182 0.52625934
|
||||
$atom:a25 $mol @atom:L 0.0 -0.83315257 1.270904 1.2564086
|
||||
$atom:a26 $mol @atom:B 0.0 -0.10469759 1.6988523 0.72597181
|
||||
$atom:a27 $mol @atom:L 0.0 -0.57854905 2.3367737 0.11206868
|
||||
}
|
||||
|
||||
} # 1beadMisfolded
|
||||
|
||||
|
||||
1beadUnfolded inherits 1beadFrustrated {
|
||||
|
||||
# This molecule "inherits" all of its features from "1beadFrustrated"
|
||||
# Here we override the atomic positions with new coordinates:
|
||||
|
||||
# AtomID MoleculeID AtomType Charge X Y Z
|
||||
|
||||
write('Data Atoms') {
|
||||
$atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0
|
||||
$atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8
|
||||
$atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8
|
||||
$atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0
|
||||
$atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0
|
||||
$atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8
|
||||
$atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8
|
||||
$atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0
|
||||
$atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0
|
||||
$atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8
|
||||
$atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8
|
||||
$atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0
|
||||
$atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0
|
||||
$atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8
|
||||
$atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8
|
||||
$atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2
|
||||
$atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2
|
||||
$atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6
|
||||
$atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6
|
||||
$atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2
|
||||
$atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2
|
||||
$atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6
|
||||
$atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6
|
||||
$atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2
|
||||
$atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2
|
||||
$atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6
|
||||
$atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6
|
||||
}
|
||||
|
||||
} # 1beadUnfolded
|
||||
|
||||
|
|
@ -0,0 +1,67 @@
|
|||
#!/usr/bin/env python
|
||||
|
||||
# Calculate a table of dihedral angle interactions used in the alpha-helix
|
||||
# and beta-sheet regions of the frustrated protein model described in
|
||||
# provided in figure 8 of the supplemental materials section of:
|
||||
# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
|
||||
# Note that the "A" and "B" parameters were incorrectly reported to be
|
||||
# 5.4*epsilon and 6.0*epsilon. The values used were 5.6 and 6.0 epsilon.
|
||||
# The phiA and phiB values were 57.29577951308232 degrees (1 rad)
|
||||
# and 180 degrees, respectively. Both expA and expB were 6.0.
|
||||
#
|
||||
# To generate the table used for the alpha-helix (1 degree resolution) use this:
|
||||
# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360
|
||||
# To generate the table used for the beta-sheets (1 degree resolution) use this:
|
||||
# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360
|
||||
#
|
||||
# (If you're curious as to why I set the location of the minima at phi_alpha
|
||||
# to 1.0 radians (57.2957795 degrees), there was no particularly good reason.
|
||||
# I think the correct value turns out to be something closer to 50 degrees.)
|
||||
|
||||
|
||||
from math import *
|
||||
import sys
|
||||
|
||||
|
||||
# The previous version included the repulsive core term
|
||||
def U(phi, A, phiA, expA, B, phiB, expB, use_radians=False):
|
||||
conv_units = pi/180.0
|
||||
if use_radians:
|
||||
conv_units = 1.0
|
||||
termA = pow(cos(0.5*(phi-phiA)*conv_units), expA)
|
||||
termB = pow(cos(0.5*(phi-phiB)*conv_units), expB)
|
||||
return -A*termA - B*termB
|
||||
|
||||
# The previous version included the repulsive core term
|
||||
def F(phi, A, phiA, expA, B, phiB, expB, use_radians=False):
|
||||
conv_units = pi/180.0
|
||||
if use_radians:
|
||||
conv_units = 1.0
|
||||
termA = (0.5*sin(0.5*(phi-phiA)*conv_units) *
|
||||
expA * pow(cos(0.5*(phi-phiA)*conv_units), expA-1.0))
|
||||
termB = (0.5*sin(0.5*(phi-phiB)*conv_units) *
|
||||
expB * pow(cos(0.5*(phi-phiB)*conv_units), expB-1.0))
|
||||
return -conv_units*(A*termA + B*termB)
|
||||
|
||||
if len(sys.argv) != 10:
|
||||
sys.stderr.write("Error: expected 9 arguments:\n"
|
||||
"\n"
|
||||
"Usage: "+sys.argv[0]+" A phiA expA B phiB expB phiMin phiMax N\n\n")
|
||||
sys.exit(-1)
|
||||
|
||||
A = float(sys.argv[1])
|
||||
phiA = float(sys.argv[2])
|
||||
expA = float(sys.argv[3])
|
||||
B = float(sys.argv[4])
|
||||
phiB = float(sys.argv[5])
|
||||
expB = float(sys.argv[6])
|
||||
phi_min = float(sys.argv[7])
|
||||
phi_max = float(sys.argv[8])
|
||||
N = int(sys.argv[9])
|
||||
|
||||
for i in range(0,N):
|
||||
phi = phi_min + i*(phi_max - phi_min)/(N-1)
|
||||
U_phi = U(phi, A, phiA, expA, B, phiB, expB, use_radians=False)
|
||||
F_phi = F(phi, A, phiA, expA, B, phiB, expB, use_radians=False)
|
||||
print(str(i+1)+' '+str(phi)+' '+str(U_phi)+' '+str(F_phi))
|
||||
|
||||
|
|
@ -0,0 +1,20 @@
|
|||
import "1beadFrustrated_variants.lt"
|
||||
|
||||
|
||||
protein = new 1beadUnfolded
|
||||
|
||||
|
||||
|
||||
# Note: The protein begins in an "Unfolded" conformation. If instead
|
||||
# you want it to begin in the folded or misfolded conformations use:
|
||||
# protein = new 1beadFrustrated # or
|
||||
# protein = new 1beadMisfolded
|
||||
|
||||
|
||||
|
||||
# ("27.0" is the length of the protein when maximally extended)
|
||||
write_once("Data Boundary") {
|
||||
0.0 27.0 xlo xhi
|
||||
0.0 27.0 ylo yhi
|
||||
0.0 27.0 zlo zhi
|
||||
}
|
||||
Some files were not shown because too many files have changed in this diff Show More
Loading…
Reference in New Issue