[gmx-users] potential energy

[Anton Feenstra]

Michal Kolinski wrote:

> Hi all.
> I did 2ns MD  of system involving TM-protein + ligand + lipids + SOL + ions.
> How can I  calculate potential energy separately for protein and separately  for ligand?

There are no energies associated with a molecule, in stead they are 
associated with interactions. So, you can have the protein-protein 
internal interaction energies, or the ligand-ligand internal (which may 
be zero), or the ligand-protein interaction energies, and so on.

'LR Coulomb' energies, are labeled 'Coul-LR' in the energy group names.

You can select multiple groups of your choice, and use an external 
program (e.g., xmgrace or awk) to add up the appropriate columns in the 
output .xvg file (or, add up the reported averages).


-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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