Dear community, Thanks again, Mark! Your comments made me realize that I was mixing two concepts and allowed me to figure out what was going on. I apologize for the confusion. The correct formulations are:
a) protein-protein (bonded and non-bonded) b) protein-solvent (interaction, non-bonded) c) solvent-solvent (interaction, non-bonded) (d) solvent bonded terms) E_pot_tot = a + b + c (+ d) [WITH NO 0.5 FACTOR] and E_pot_prot = a + 0.5*b ...where E_pot_prot would define the potential energy of a protein subsystem, including all protein bonded terms, all protein to protein interactions, as well as all solvent to protein (and not protein to solvent, therefore the term *0.5). In order to cross-check this formulation, I was summing up potential energy contributions. Although I use SHAKE constraints to describe bonds and angles, my SPC water is rigid, since I have not set "defines" to "-DFLEXIBLE" in my input file. So it IS normal that I obtain the same values for bonded potential energy terms in the log file and from g_energy uppon request of protein terms. I guess rigid SPC bonding energy terms, which would never vary, are simply not counted in the total potential energy. In my case, "d" is thus equal to 0. But the "RF excl." term (removing RF correction for "1-4" electrostatic interactions and other excluded pairs) also has to be added in order to get the final sum correct. If I call this term "e", we get: E_pot_tot = a + b + c + e Dose anybody know if this last term, "RF excl", is computed / written separately for protein / water atoms? I would be interested in the "RF excl" contributions coming from protein atoms only.. Are there such terms for intra-molecular water to water atom interactions also, or are they limited to the "1-4" interactions of the protein? In the first case, I guess they would not be counted anyway, with my rigid SPC water? Thanks for any feedback! 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
