Dear Justin, I've tried what you have suggested. I have used the pull code and gave 4 amino acid residues as a reference group. The location of the groups are one below the ligand (in the protein core) and 3 were on the above ( towards the active site gorge). When i used the code
pull = umbrella pull_geometry = distance ; simple distance increase pull_start = yes ; define initial COM distance > 0 pull_ngroups = 1 pull_group0 = DRG pull_group1 = reference groups pull_rate1 = 0.003 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 the ligand migrated more and more towards the protein , not coming out of the protein through the channel i defined by referring the amino acid groups when I tried with pull_geometry = position, the pull_vec i gave as 0 0 1 and pull_initial = 0.1 but the grompp ends up with an error saying pull_vec can not be zero. when i was trying to use pull_geometry = direction the system blowed up. but the pull_geometry = distance worked well. please give me a suggestion to resolve the issue -- View this message in context: http://gromacs.5086.n6.nabble.com/COM-Pulling-tp4998944p4998989.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
