On Sat, Nov 15, 2025, Surabhi Singh 24933024 via AMBER wrote:
>I’m running a protein–ligand simulation. The equilibration (on CPU) and
>production run (on GPU) both completed smoothly. However, when I run the
>same system’s equilibration using pmemd.MPI, I encounter a problem
>specifically during the NPT step.
>
> - MPI seems to be working correctly, as minimization and NVT steps both
> completed without any issues.
> - The box dimensions and parameters should be fine, since the same setup
> runs successfully without MPI.
See if the problem goes away if you set barostat=2 in the NPT runs. There
have been reports of pmemd.MPI problems when the default barostat is used.
(Barostat=2 should really be the default, but that would lead to problems
of backwards incompatibility.)
....dac
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Received on Sat Nov 15 2025 - 07:30:03 PST
