On Mon, Jun 30, 2025, Delwakkada Liyanage, Senal Dinuka via AMBER wrote:
>
>I'm facing instability when continuing a trajectory using the Berendsen
>barostat on a GPU cluster.
>
>System: POPC bilayer (288 lipids) in ~8000 choline geranate molecules (box
>size ~100 × 100 × 200 ų)
>
>What I did:
>
>Performed 5 ns NPT equilibration on CPU (local machine).
>Continued for 1 ns on:
>
>
> *
>Local GPU (GTX TITAN, Amber 20) – completed successfully.
> *
>Cluster GPU (A100 MIG, Amber 24) – crashes almost immediately.
Instead of "continuing for 1 ns", continue the simulation (on both GPUs) for
(say) 100 steps, setting ntpr=1. Carefully compare the outputs to try to
localize what the differences are. This will also help to determine what the
"almost immediately" phrase really means.
>
>ERROR: Calculation halted. Periodic box dimensions have changed too much
>from their initial values.
Setting ntpr=1 will also help to see in detail what the periodic box
dimensions are actually doing.
If you don't see differences in 100 steps, try larger number of steps, but
keep ntpr=1. It may also be worth trying these short runs on a CPU as well,
but a (good)GPU vs (bad)GPU comparison is likely to be of more use.
...good luck....dac
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Received on Sun Jun 29 2025 - 19:30:02 PDT
