Maybe you know how do they keep nanotubes rigid then?
On Wed, Feb 5, 2014 at 3:58 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.