[gmx-users] Total potential energy: 1/2 protein-solvent interactions??

pascal.baillod at epfl.ch pascal.baillod at epfl.ch
Wed Mar 5 20:38:59 CET 2008

Dear developers,

I would like to know the exact definition of the total potential energy with
respect to protein-solvent interactions, in an explicit solvent protein simulation.

For protein atom Pm and solvent atom Wn, there are two interactions:

Pm to Wn
Wn to Pm

Are both interaction energies counted in the total potential energy given in the
log file or by g_energy?

If I want to compute the total potential enery of the protein, plus
protein-solvent interactions, should I then only add half of the protein-solvent
terms given by g_energy? I am only interested in the effect of solvent "felt" by
the protein, and not in the effect of the protein felt by the solvent.

Thank you very much for your help!


Pascal Baillod (PhD student) 
Swiss Federal Institute of Technology EPFL	        Tel: +41-(0)21-693-0322
Institute of Chemical Sciences and Engineering ,	Fax: +41-(0)21-693-0320
Laboratory of Computational Chemistry and Biochemistry	pascal.baillod at epfl.ch
Room BCH 4121, Avenue Forel,	                        http://lcbcpc21.epfl.ch
CH-1015 Lausanne	

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