Re: [gmx-users] option for finding forces between two groups
Pradip Biswas wrote: Hi, Anyone can please tell me whether there is any option in GROMACS to find forces between two groups (say for example, between two residues in a protein or between a peptide and a residue in a Protein for Protein-peptide interaction) or one need to workaround with the code to get that? Probably you should do a rerun with energy group exclusions used properly. See section 7.3 of the manual. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] option for finding forces between two groups
Work with groups and an index file, and define energy_groups in the mdp file also. For indices, check make_ndx utility. Omer. Koby Levy research group, Weizmann Institute of Science. FAX: 972-77-444-7905 http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Fri, Oct 2, 2009 at 20:31, Pradip Biswas biswas...@gmail.com wrote: Hi, Anyone can please tell me whether there is any option in GROMACS to find forces between two groups (say for example, between two residues in a protein or between a peptide and a residue in a Protein for Protein-peptide interaction) or one need to workaround with the code to get that? Thanks in advance. Biswas. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] option for finding forces between two groups
Hi, Anyone can please tell me whether there is any option in GROMACS to find forces between two groups (say for example, between two residues in a protein or between a peptide and a residue in a Protein for Protein-peptide interaction) or one need to workaround with the code to get that? Thanks in advance. Biswas. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
