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.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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