script to convert GROMACS tpr to psf/prm

Peter pmam... at gmail.com
Sat Aug 28 13:51:54 CEST 2010


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]) 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].

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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