script to convert GROMACS tpr to psf/prm

Peter pmam... at gmail.com
Sat Dec 13 13:59:01 CET 2014


Dear cp2k users,

Since a few people asked me to share the tpr2psf script, here is the 
link: https://github.com/pmamonov/tpr2psf

Regards,
Peter

On Saturday, August 28, 2010 3:51:54 PM UTC+4, Peter wrote:
>
> Dear All, 
> Some time ago I wrote a (python) code to convert GROMACS binary TPR 
> files into CP2K readable PSF (topology) and PRM (FF parameters) files. 
> Unfortunately I didn't achieve exact match between energies calculated 
> by GROMACS and CP2K/FIST. Respective energies calculated by GROMACS 
> and CP2K/FIST match in case of bonds, angles and sometimes dihedrals. 
> Nonbonded interactions (Coulomb and VdW, both long range and 1-4) are 
> different for most of tested systems. Gradients calculated by both 
> codes for some large system correlate with covariance coefficient 0.4. 
> At some point I considered this result satisfactory and moved on. For 
> now I don't have an intention to further improve this conversion tool, 
> but probably others will find it to be a good starting point for 
> creating such a conversion tool or probably try it as-is. So I put an 
> archive with script, auxillary library (modified libgmx wrapper by 
> Martin Hofling [http://oldwww.gromacs.org/pipermail/gmx-developers/ 
> 2009-March/003183.html 
> <http://oldwww.gromacs.org/pipermail/gmx-developers/2009-March/003183.html>]) 
> and some sample files here: 
> http://groups.google.com/group/cp2k/web/gmx2psf.tar.bz2 
>
> Best regards, 
> Peter Mamonov 
> Lomonosov Moscow State University 
> Biological faculty 
> biophysics dept. 
>
> P.S. Here is a help message from script, which provides some 
> additional info: 
>
> ABOUT: 
> This script  reads GROMACS .tpr file and produces .psf and .prm files 
> readable by  CP2K[ http://cp2k.berlios.de/] and probably some other MM 
> software. 
> This script uses modified version of GROMACS library python wrapper, 
> written by Martin Hofling  [http://oldwww.gromacs.org/pipermail/gmx- 
> developers/2009-March/003183.html 
> <http://oldwww.gromacs.org/pipermail/gmx-developers/2009-March/003183.html>]. 
>
>
> NB: This script IS NOT capable of exact conversion between tpr and psf/ 
> prm topology/force field representation. Respective energies 
> calculated by GROMACS and CP2K/FIST match in case of bonds, angles and 
> sometimes dihedrals. Nonbonded interactions (Coulomb and VdW, both 
> long range and 1-4) are different for most of tested systems. 
> Gradients calculated by both codes for some large system correlate 
> with covariance coefficient 0.4. 
>
> REQUIREMENTS: 
> * GROMACS dynamic libraries (libgmx*.so) 
> * Modified version of GromPy wrapper (distributed  with this script) 
>
> USAGE: tpr2psf.py system.tpr 
> Will produce system.psf and system.prm 
>
>
>
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