COGRIMEN 2.0

Patch file

Teaser: COGRIMEN 2.0 with additional membrane settings will be available here.

COGRIMEN 1.0

Patch file

This patch file is prepared for integration with NAMD 2.14 which is work of The Theoretical and Computational Biophysics Group ("TCBG") from University of Illinois.

NAMD 2.14 license is available at http://www.ks.uiuc.edu/Research/namd/license.html. NAMD 2.14 and COGRIMEN 1.0 patch are licenseed with Non-Exclusive, Non-Commercial Use License. You cannot sell integrated part or whole COGRIMEN 1.0 patch.

THE SOFTWARE COGRIMEN 1.0 PATCH IS PROVIDED "AS IS" AND WITHOUT WARRANTY OF ANY KIND.

NAMD homepage: http://www.ks.uiuc.edu/Research/namd/.

Please cite NAMD as described on: http://www.ks.uiuc.edu/Research/namd/papers.html.

COGRIMEN 1.0 patch:
"This software includes code developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign."

To download COGRIMEN 1.0 patch, click button below:
I understand and agree with the license of COGRIMEN 1.0 patch.

MD5 sum: 88c5c1b8b90a895edbf203425715f17e cogrimen1.0_patch_namd2.14.tar.gz

COGRIMEN

Build notes

Steps list:

1. Download NAMD 2.14 source code from: NAMD downloads page or direct link.
2. Unpack tar xfz NAMD_2.14_Source.tar.gz
3. Copy cogrimen1.0_patch_namd2.14.patch inside extracted in previous step directory.
4. From there, run patch -p0 < cogrimen1.0_patch_namd2.14.patch command.
5. Compile according to notes.txt included in NAMD 2.14 source package.

Hints while compiling on Ubuntu 20.04:

• COGRIMEN patch was tested for NAMD 2.14 on CUDA Toolkit 11.
• Do not use sfftw from notes.txt. It will cause linking errors related to -fPIC. You can use apt install sfftw-dev.

COGRIMEN

Model files

Solvent file

Parametrization file for solvent with parameters retrived after minimization of our evaulation function (to minimization we utilize Genetic Algorithm from DEAP/scoop bundle, more infomation in our COGRIMEN paper). This file must be pointed in CGIMSolventFile variable. Download

Force field parameters files

Coarse-grained force field parameters. Download

COGRIMEN

Tutorial

New input file variables

• CGIM - Is COGRIMEN enabled? [yes/no]
• CGIMSolventFile - filename of COGRIMEN model solvent file [filename] - available to download in Model files
• CGIMMembrane - Is membrane enabled or only water? [yes/no]
• CGIMMembraneWidth - Membrane width [Å]
• CGIMAEMPIR - value of a [0.85]
• CGIMPower - value of power in switching function [10]
• CGIMCutoff - additional COGRIMEN computations cutoff [9.0]
• CGIMGsolvOut - print to log gsolv values [yes/no]
• CGIMGsolvOutFirstNum - when start printing gsolv values - fe. avoid printing in minimization [1]

Values: [], default. There is hierarchy in compulsory of arguments, fe. if CGIMMembrane is set to no, then CGIMMembraneWidth is not needed.

Preparing new structure for coarse-grained MD

Could be done with our scripts package gene-tools which provide preparation process based on instructions described on NAMD Tutorials page in Residue-Based Coarse-Graining. Direct link to PDF, tutorial files. Additional infomations on MARTINI General Purpose Coarse-Grained Force Field page. Direct link to tutorials.

Preliminaries.

1. Download our scripts package gene-tools.tar.gz
2. tar -xf gene-tools.tar.gz
3. cd gene-tools
4. Download tutorial file (files.tar.gz) to gene-tools directory
5. tar -xf files.tar.gz
6. files prepare.sh, martini_nomed.namd, solvpar_martini_COGRIMEN.inp, and martini-par_COGRIMEN should be existing in gene-tools directory.
7. execute script: ./prepare.sh
What it does:
It generates $DIRNAME directory (by default it is called prepare).
It contains several modified files from tutorial package.
8. What next:
In gene_martini.sh set a path to prepare directory (variable: $GENE_MARTINI_PATH)
[ You can keep gene_martini.sh wherever you want, e.g. ~/bin]

Preparing files for simulations.

1. If your system is an individual chain:
   ./gene_martini.sh 1tit.pdb 1TIT
   [first argument: pdb file name, second argument: any string used in naming temporary files]
   The final files are protein.pdb, and protein.psf
2. When there are several chains, then prior to generating CG files one has to:
   1. split chains into seprarate files [ example script: generate_separate_chains.tcl ]
      vmd -dispdev text -e generate_separate_chains.tcl
   2. merge these chains together: [ example script: merge_chains.tcl ]
      vmd -dispdev text -e merge_chains.tcl
      There are PDB and PSF files generated. In this example I used structure with PDB id: 1afo (first model).
      (Be careful with file names and segname names, like PROA, PROB, etc.)
   3. Finally generating CG files: ./gene_martini.sh 1afo0seg.pdb 1AFO 1afo0seg.psf

Now instantly you can test the system by running short simulation using a simplified input file, e.g.:
namd2 +p4 martini_nomem.namd > namd.log
[namd2 stays for NAMD with COGRIMEN patch executive you have installed]

COGRIMEN

Example files

Example PDBID:4G7V

Coarse-grained 4G7V model example NAMD input file with COGRIMEN variables set bundled with COGRIMEN model files. Ready to run. Download

COGRIMEN

How to cite

COGRIMEN: Coarse-Grained Method for Modeling of Membrane Proteins in Implicit Environments
Przemysław Miszta, Paweł Pasznik, Szymon Niewieczerzał, Krzysztof Młynarczyk, and Sławomir Filipek

Journal of Chemical Theory and Computation 2022 18 (9), 5145-5156
DOI: 10.1021/acs.jctc.2c00140

When using COGRIMEN please cite also NAMD as described on: http://www.ks.uiuc.edu/Research/namd/papers.html.