On 25/11/2011 2:28 AM, Vasileios Tatsis wrote:
Dear Gromacs Users,
I am using the -rerun option of mdrun to re-analyze a trajectory.
Thus, I tried to rerun the same trajectory (md.xtc) with exactly the
same md.tpr.
But the bonded interactions are not computed or written to the log
file or to the .edr file, resulting to completely different energy
values from the initial log and edr files.
That does not sound possible if the .tpr is the same. With bond or angle
constraints, some bonded terms would not appear in either version, of
course.
Mark
I am using the following command, in order to read the coordinates stored in
the .xtc file and compute the potential energy:
mdrun -rerun md.xtc -s md.tpr
Thanks in advance for your help
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