Dear David, In fact I really did as you said. First prepare a top file which explicitly include all bonded and nonbonded terms according to combination rule. In this way that top file can be called stand-alone top file (all the necessary parameters all included). Then you can do what you want. In my case I modify 1,4 interaction.
Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David Mobley Sent: Friday, April 06, 2007 2:20 AM To: Discussion list for GROMACS users Subject: [gmx-users] modify C6 directly in FF using sigma and epsilon Gromacs users, I'm using a force field (the port of AMBER to GROMACS) which uses combination rules (combination rule 2), etc. in terms of sigma and epsilon. However, I need to be able to modify C6 directly (in particular, I want to be able to set it to zero). Can anyone give me any pointers on a relatively straightforward way to do that? I want to be able to continue using combination rule 2 but be able to separately modify C6 for a couple atom types (or interacting atom pairs). Obviously, one way I could work around this would be to explicitly specify all of the nonbonded interaction pairs in my topology so that the combination rules aren't used, then I could change the combination rule so that I could modify C6 and C12. But since that would be a real pain I'm hoping someone here can suggest something easier. Thanks, David _______________________________________________ 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 _______________________________________________ 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
