Dr. Case,
I found a previous post (
http://archive.ambermd.org/201804/0323.html <
http://archive.ambermd.org/201804/0323.html>) 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?
Best,
Matthew
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Received on Wed Jan 06 2021 - 01:00:02 PST
