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
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