Hi gromacs people,
I was trying to rerun old xtc trajectories to recalculate some energies
involving the solvent, using gmx 3.3.1. I saw important discrepancies
with the original energies (nstlist=1, xtc unaccuracy tolerated). After
some struggling, I figured out that the box size is determined form the
.gro file used to create the .tpr file, and are not read from the
trajectory. I then realized that this problem had been described two
years ago on the list:
http://www.gromacs.org/pipermail/gmx-users/2005-October/017729.html
The issue was then transferred to bugzilla :
http://bugzilla.gromacs.org/show_bug.cgi?id=26
and a patched md.c was proposed by David, apparently for gromacs 3.3.0.
It seems that this patch has not been integrated in gmx 3.3.1, because
the -rerun option still gives wrong energies. What's worse, the patched
md.c cannot be used for 3.3.1, because apparently the number of
arguments for init_md() has changed.
Could someone work out a patch for 3.3.1, and maybe post it on the same
bugzilla thread?
I think this bug should be mentioned in the "known bugs" section of the
website. That would probably save some sweat to others like me trying to
use the -rerun option...
Thanks,
Michel
--
==========================================================
Michel Cuendet, Ph.D
Molecular Modeling Group
Swiss Institute of Bioinformatics
CH-1015 Lausanne, Switzerland
www.isb-sib.ch/groups/Molecular_Modeling.htm
==========================================================
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