[gmx-users] Vacuum simulation in Gromacs 5

[Justin Lemkul]

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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