On 3/11/15 8:58 PM, Ming Tang wrote:
Dear Justin, Thanks for your help. I changed the group names to Chain_A and Chain_B in my index file, and modified the COM pulling code. ; COM pulling pull = umbrella pull_geometry = distance ; simple distance increase pull_dim = N N Y pull_start = yes ; define initial COM distance > 0 pull-ngroups = 1 ?assign the reference group? pull-group1-name = Chain_A pull-coord1-rate = 0.01 ; 0.01 nm per ps = 10 nm per ns pull-coord1-k = 1000 ; kJ mol^-1 nm^-2 But I didn't found the order to assign the reference group Chain_B in GROMACS 5.0.4 Could you give me some help?
Something like this (I haven't tested it, so please let me know if this works...or doesn't):
pull = umbrella pull-geometry = distance pull-dim = N N Y pull-start = yes pull-ngroups = 2 pull-ncoords = 1 pull-coord1-groups = 1 2 pull-group1-name = Chain_A pull-group2-name = Chain_B pull-coord1-rate = 0.01 pull-coord1-k = 1000 -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
