On Fri, Nov 08, 2024, Maciej Spiegel via AMBER wrote:
>Encountered error: „ERROR: Calculation halted. Periodic box dimensions
>have changed too much from their initial values.
> Your system density has likely changed by a large amount, probably from
> starting the simulation from a structure a long way from equilibrium."
>
>I run my simulations in 10 x 10 ns jobs using GPU. They keep failing at
>various stages, not just at the first interval—one job even terminated
>in the 9th interval! Although the errors suggest this might be due to
>significant density fluctuations, the density remains within the range of
>1.0355 to 1.0383. I inspected the MD trajectory and didn’t notice any
>specific issues.
>I use H-mass repartitioned topology generated with CPPTRAJ.
It might help to know exactly how you applied H-mass repartitioning. Have
you checked the masses in the prmtop file (with an editor, or with parmed)
to make sure they are OK?
A second idea, longshot: try some runs with NVT rather than NPT: does the
problem go away? If it does, try NPT but with barostat=2.
But overall, it looks like something is triggering a failure, and doing
enough damage to lead to an incorrect error message. Others on the list may
see something that rings a bell. But we may need to get enough files to try
to reproduce the problem.
...good luck...dac
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Received on Fri Nov 08 2024 - 16:30:03 PST
