script to convert GROMACS tpr to psf/prm
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
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/
> and some sample files here:
> 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:
> This script reads GROMACS .tpr file and produces .psf and .prm files
> readable by CP2K[ http://cp2k.berlios.de/] and probably some other MM
> This script uses modified version of GROMACS library python wrapper,
> written by Martin Hofling [http://oldwww.gromacs.org/pipermail/gmx-
> 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.
> * 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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