[gmx-users] Vacuum simulation in Gromacs 5

[David van der Spoel]

On 11/06/15 11:53, 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 grid search in any case. It supports vacuum.

> Thank you,
> Jan
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se