Dear All,
I want to pulling a ligand out of the binding pocket using Gromacs 2019. The pulling code was: pull = yes pull_ncoords = 1 pull_coord1_type = umbrella pull_coord1_geometry = direction pull_ngroups = 1 pull_group1_name = Ligand pull_coord1_dim = Y N N pull-coord1-vec = 1 0 0 pull_coord1_rate = 0.0005 pull_coord1_k = 830 I think the reaction coordinate had been defined by COM of the pulling group (i.e the ligand) and the pulling direction vector (i.e 1 0 0), but why still need to provide two groups for pull_coord1_groups ? If provided, then the reaction coordinate was also defined by the COM of the two groups, is this right? How should I set up my pulling code with "pull_coord1_geometry = direction". Any suggestion would be appreciated! Best regards Sting -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
