[gmx-users] Vacuum simulation in Gromacs 5

[Jan Jirsák]

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?

Thank you,
Jan