Dear community, Thanks again for these most helpful explanations, Berk! If I understood everything correctly, the following questions could be answers..
1) I would like to know why the RF correction of 1-4 interacting atoms was counted in another term, RF-excl. If I understand well, it is not correct to add this interaction to the total potential energy of atoms, from which atomic forces will be derived, since 1-4 electrostatic interactions are too strong. So the RF-excl term would just be a control and is added to no potential energy at all? If it is added, in what way is that done differently than in versions older than 3.3.? 2) The RF-excl term is an addition of all excluded pair interactions, from the solvent and from the protein. I guess the biggest part of the RF-excl term would come from the solvent self pair interactions, in this case? Thank you very much for your patience! Best regards, 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
