[gmx-users] potential energy

[Tom Dupree]

Greetings all,

Can I easily obtain the potential energy for a energy group rather than the whole simulation cell? Does it make any sense to do so?
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.

Have fun,
Tom