[gmx-users] mdrun -rerun (not reproducible energy values?)

[Mark Abraham]

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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