Dear community, Thanks, Mark! But I can't find any g_energy or log file terms specifically related to solvent bonded energy (bonds and angles). The log file bonded terms are for the total system, I guess, but they are very close to the ones I get when I request their "protein" counterpart from g_energy. My guess would be that, in my 103-residue protein (1142 at) system solvated by 14'076 water molecules (42'228 at), there should be a large difference between protein bonded and solvent bonded terms.
Perhaps water bonded terms are not counted at all, as the water molecule geometry dose not vary with the SPC model, during the simulation? By the way, is the assumption of my previous mail correct? The one on the total potential energy formulation as a function of g_energy potential energy decomposition terms: Etot = a + 0.5*b + c (+ d), with a) protein-protein (bonded and non-bonded) b) protein-solvent (interaction, non-bonded) c) solvent-solvent (interaction, non-bonded) (d) solvent bonded terms) (Of course this only holds when using a non-PME method (i.e. generalised reaction field) for long range electrostatics!) Thank you very much for any info!! 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 [email protected] 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
