Depends on the size of your system and how much parallelism you want to use. See manual section on DD.
Mark On Wed, Feb 5, 2014 at 4:58 PM, Steven Neumann <s.neuman...@gmail.com>wrote: > Thank you. Can you specify what does long mean? Is there any limit? > > > On Wed, Feb 5, 2014 at 3:49 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > 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. > > > -- > 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.