GROMACS modification: Yes/No
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I have done 200 ns MD for membranes and nanoparticles and I want to do the MSD calculations, but in the 194 ns process was killed. What is the cause and how is it solved?
Hard to say with limited data, but on login nodes of many clusters, admins will often automatically kill analysis jobs that run for longer than some threshold. I imagine this might be your case.
Anyway, how is the title related to the actual question?
thanks for your response. I do the calculations on my personal system and I am the admin.
Hi, this is almost certainly an out-of-memory error. gmx msd has to save every frame to back-calculate long MSDs, and you’re probably hitting a limit.
Right now, you can reduce the number of frames saved by increasing the value of the -trestart option.
In Gromacs 2022, I’m planning to add an option to cap the max “tau” value for MSD comparison, to reduce memory, but that won’t be available for a while.