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.
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