[gmx-users] position restraint
Mark.Abraham at anu.edu.au
Sun Sep 4 01:36:24 CEST 2011
On 4/09/2011 1:44 AM, Kun Huang wrote:
> Dear Gromacs users:
> I am trying to extract the constraint energy imposed by position
> restraint. I extract the coordinate of the restraint atom and want to
> calculated directly by using the harmonic potential.
You can do this fairly easily with mdrun -rerun on the old trajectory
with a new .tpr, leaving only the position restraint of interest intact
in the new .tpr. Now the .log file will have that energy.
> The question is : Does the reference position come from the .gro file
> as the input in mdrun? It seems to me that that's the only possible
> source as I didn't specify it anywhere.
It defaults to the input coordinate file to grompp, but can be specified
otherwise. See grompp -h.
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