On 2/5/14, 10:46 AM, Steven Neumann wrote:
Can you please advise? With large constraints it does not work... with [ distance_restraints ] it works but only with mdrun -nt 1 my mdp: disre = simple disre-fc = 1000 integrator = md tinit = 0.0 dt = 0.008 nsteps = 100000 ; 500 ns nstcomm = 100 nstcalcenergy = 100 nstxout = 0 nstvout = 0 nstenergy = 0 nstlog = 100 nstxtcout = 100 freezegrps = System freezedim = N N Y energygrps = ACI BAS GLY NON POL energygrp_table = ACI ACI ACI BAS ACI GLY ACI NON ACI POL BAS BAS BAS GLY GLY GLY GLY NON GLY POL NON BAS NON NON POL BAS POL NON POL POL table-extension = 1.0 nstlist = 10 ns_type = grid pbc = xyz rlist = 2.0 coulombtype = User rcoulomb = 2.0 vdw_type = User rvdw = 2.0 tcoupl = V-rescale tc_grps = System tau_t = 0.1 ref_t = 300 pcoupl = no gen_vel = yes gen_temp = 300 gen_seed = -1 constraints = none constraint_algorithm = Lincs continuation = no lincs_iter = 1 lincs_order = 4 I will really appreciate.
DD cells are set up based on bonded geometry and a host of other factors. Any very long bond or restraint will seriously inhibit the ability of DD to function.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. 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.
