Re: [AMBER] Setting PME cutoff in Crystal Simulations

From: Matthew Guberman-Pfeffer <>
Date: Wed, 6 Jan 2021 03:33:05 -0500

Dr. Case,

I found a previous post ( <>) about the error message I reproduced and posted earlier. My system starts out the NPT equilibration with dimensions (129.600 32.400 101.100). The calculation proceeded until timing out on the HPC. When I restarted the calculation, the system had dimensions (128.374 32.093 100.143). I understood from the other post that the ~30 Å dimension is problematical (why is still a bit unclear to me). I also wonder what would have happened if I simply allocated more time for the calculation. Are my options either to make the system larger, run on CPUs instead of GPUS, or is there another way forward?

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Received on Wed Jan 06 2021 - 01:00:02 PST
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