[gmx-users] potential energy

[Mark Abraham]

On 14/08/2012 11:07 AM, Tom Dupree wrote:
> Greetings all,
>
> Can I easily obtain the potential energy for a energy group rather than the whole simulation cell?

Yes. See manual 3.3 and 7.3.8. But below you imply you're already doing 
this. You can make custom groups - see 
http://www.gromacs.org/Documentation/File_Formats/Index_File

>   Does it make any sense to do so?

Doubt it.

> I am simulating protein ligand complexes and have observed movement in some cases. When I analyse the interaction energy sum of LJ and columbic of LIG-rest (or Lig-Protein + Lig-rest) I get very flat energy plots with no significant differences between the runs where movement occurs and runs where it does not.
> I am wondering if there are some energy terms I have not accounted for that may explain the differences and thought potential energy may be one. However any changes in ligand potential energy are going to be dwarfed by protein and water changes.

You can't expect to get an accurate quantitative picture by only looking 
at changes in internal energy, or only such changes for part of the 
system, because you have no estimate for how often those configurations 
arise. If the statistics from multiple runs of the same ensemble are 
significantly different, then you know you haven't converged any of the 
runs, and so probably can't say anything sensible about them.

Mark