The error 3 was solved, but when I change to cutoff-scheme = group, I receive:
"Fatal error: The largest charge group contains 66 atoms. The maximum is 32." I've tried to make this before, and I saw your answer about this error in this link: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2011-June/061989.html But I don't understand what I need to do. 2017-03-27 17:56 GMT-03:00 Justin Lemkul <jalem...@vt.edu>: > > > On 3/27/17 4:50 PM, Graziele Bortolini wrote: > >> I do it too, my .mdp file now is like : >> ----- >> cpp = /lib/cpp >> integrator = md >> dt = 0.001 >> nsteps = 500000 >> nstcomm = 1 >> comm-mode = angular >> nstxout = 0 >> nstvout = 0 >> nstlog = 0 >> nstenergy = 50 >> nstxtcout = 50 >> energygrps = PSB >> nstlist = 10 >> ns_type = grid >> rlist = 0 >> coulombtype = Cut-off >> optimize_fft = yes >> rcoulomb = 0 >> vdwtype = shift >> rvdw = 0 >> tcoupl = berendsen >> tc_grps = system >> ref_t = 300.0 >> tau_t = 0.1 >> pcoupl = berendsen >> ref_p = 1.000 >> compressibility = 4.5e-5 >> tau_p = 1.0 >> pcoupltype = isotropic >> gen_vel = yes >> gen_temp = 300.0 >> pbc = no >> ------ >> but I receive another errors messages: >> >> >> ERROR 1 [file teste2.mdp]: >> With Verlet lists only full pbc or pbc=xy with walls is supported >> >> ERROR 2 [file teste2.mdp]: >> The box volume is required for calculating rlist from the energy drift >> with verlet-buffer-tolerance > 0. You are using at least one unbounded >> dimension, so no volume can be computed. Either use a finite box, or set >> rlist yourself together with verlet-buffer-tolerance = -1. >> >> > Both of these are solved with cutoff-scheme = group. > > ERROR 3 [file teste2.mdp]: >> With switched vdw forces or potentials, rvdw-switch must be < rvdw >> >> > You have an infinite cutoff, there's nothing to switch or shift. You need > vdwtype = cutoff. > > > -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. > -- Att. G. Bortolini -- 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.