Thanks for your reply Justin. >From your umbrella tutorial I thought the reference group should be the protein. Now from your reply i think I can specify any amino acid residue in the protein and I can drive the ligand towards the residue. where I need to specify the group
If i'm using the pull code ; Pull code pull = umbrella pull_geometry = distance ; simple distance increase pull_dim = N N Y pull_start = yes ; define initial COM distance > 0 pull_ngroups = 1 pull_group0 = DRG pull_group1 = ?? pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 how can i specify the residue if i want to pull towards the direction of 3 amino acids, and I've included in the index file please help... -- View this message in context: http://gromacs.5086.n6.nabble.com/COM-Pulling-tp4998944p4998955.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
