[gmx-users] dt in mdp

[Alex]

Dear all,
After minimization and equalizations using nvt (v-rescale) and npt (both
berendsen and ;Parrinello-Rahman), a simulation of mine could run well for
200 ns using dt =0.001 while it would crash after 3 ns If I used dt = 0.002
with the particles communication fatal error.

Fatal error:
2 particles communicated to PME rank 12 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension y.
This usually means that your system is not well equilibrated.

So, if the system would not be well equlibrated, then I would expect that
with dt = 0.001 the simulation wouldn't run well for 200 ns. But I expect
that it also crashes for example around 6 ns as the with the dt = 0.002 the
simulation last only 3 ns.

Any comment that helps to understand the problem would be highly
appreciated.
Regards,
Alex