On 4/24/14, 5:21 AM, Kalyanashis wrote:
Dear all, I am doing SMD simulation of a enzyme system and I have given the pull option in Z direction. The com pulling options are given below, ;COM pulling pull = umbrella pull_geometry = distance pull_dim = N N Y pull_r1 = 1 pull_r0 = 1 ;pull_constr_tot = 1e-6 pull_start = yes pull_nstxout = 10 pull_nstfout = 1 pull_ngroups = 1 ;name of reference group pull_group0 = Protein ;pull_weights = 0 ;name of pull group pull_group1 = UNK ;pull_weights = 0 pull_vec1 = 0.0 0.0 -1 ;ref. distance at t=0 ;pull_init1 = -2.4477384 -1.0229216 -1.5900776 ;rate of change of ref. gr. [nm/ps] pull_rate1 = 0.0005 ;force constant [KJ mol^-1 nm^-2] pull_k1 = 1586.747 ;pull_kB1 = Please kindly tell me, how can I do the same calculation in reverse Z direction??
Change the sign of the pulling vector. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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.
