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 ******************************************************************************* 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 [EMAIL PROTECTED] Room BCH 4121, Avenue Forel, http://lcbcpc21.epfl.ch CH-1015 Lausanne ******************************************************************************* _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
