[gmx-users] position restraint

Mark Abraham 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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