Dear Justin, The results turned out that the COM distance between them is the same over time, seems that both Chain_A and Chain_B had been pulled by the same force in the same direction, which is different from the tutorial.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Ming Tang Sent: Thursday, 12 March 2015 11:34 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] umbrella sampling tutorial Hi Justin, Your code works! Thank you very much. Regards, Ming -----Original Message----- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Thursday, 12 March 2015 11:18 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] umbrella sampling tutorial 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. -- 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. -- 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.
