[gmx-users] potential energy
feenstra at few.vu.nl
Wed May 11 13:40:46 CEST 2005
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).
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