[gmx-users] dt in mdp

[Justin Lemkul]

On 4/7/20 5:00 PM, Alex wrote:
> 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.

Please provide a description of what your system is and a full .mdp 
file. While most of the time these crashes come from poor equilibration, 
an inadequately parametrized topology or bad combination/misuse of 
algorithms can also cause crashes.

-Justin

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Justin A. Lemkul, Ph.D.
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