On 6/11/15 5:53 AM, Jan Jirsák wrote:
Hello everyone, what is the correct setup for simulations with no PBC and no cuttoffs in Gromacs 5.0.4? In versions 4.5 and 4.6 i used nstlist = 0 ns_type = simple pbc = no This no longer works, as I get the error: "Domain decomposition does not support simple neighbor searching, use grid searching or run with one MPI rank" (... and particle decomposition i no longer available.) However, when I run mdrun -nt 16 -ntmpi 1 (is this correct specification for 1 MPI rank?) I get the error that OpenMP can be used only with cutoffscheme=Verlet, which in turn is not available for pbc = no. Grid searching is nonsense in this situation, as cuttoffs are infinite. I seem to be in a dead end. Does anybody know a solution?
Use mdrun -nt 1 -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.
