Re: [AMBER] Restart the crashed MD run in Amber18

From: David A Case <>
Date: Wed, 16 Jun 2021 09:00:52 -0400

On Wed, Jun 16, 2021, Amir Zeb wrote:
>in the restrated simulation. The job restarted
>successfully but stopped/crashed again after some time. Would you please
>let me know how I can find the reason for this crash?

So, now it seems that the instability is reproducible. How long does it
take after the restart before you encounter problems? It's often useful
to run shorter simulations with small values of ntpr to get more detailed

One place to start is to use the "checkstructure" action in cpptraj on the
restart coordinates. That might flag problems.

> nstlim=200000000,
> ntpr=10000,

Consider *much* shorter runs, setting ntpr to 10 or 100. Your goal is to
collect some information near the point at which the crash happens.


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Received on Wed Jun 16 2021 - 06:30:03 PDT
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