[gmx-users] mdrun -rerun and box size bug not fixed?
michel.cuendet at isb-sib.ch
Thu Nov 1 11:23:36 CET 2007
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:
The issue was then transferred to bugzilla :
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
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...
Michel Cuendet, Ph.D
Molecular Modeling Group
Swiss Institute of Bioinformatics
CH-1015 Lausanne, Switzerland
More information about the gromacs.org_gmx-users