Re: [AMBER] Automated restart

From: David A Case <>
Date: Sat, 8 Aug 2015 08:42:16 -0400

On Sat, Aug 08, 2015, Eugene Radchenko wrote:
> I have encountered the "Calculation halted. Periodic box dimensions have
> changed too much from their initial values" error and see an advice here
> to restart the calculation from
> the latest restart file.
> Actually I think it would be nice if pmemd.cuda could reset the grid
> automatically when such condition occurs.

We might consider this, but this should be a rare event; or maybe it becomes
more common for certain types of simulations(?). Are you seeing this a lot?
Is there something unusual about the types of systems you are simulating?
Does this happen at the very beginning of your equilibration, or at later

> But failing that, is there a nice way to automate the restart? In other
> words, how to determine the right number of steps for the restarted
> simulation?

I'm not sure I understand your request. There is no (obvious) "right number"
of steps when you continue, as far as I can see.


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Received on Sat Aug 08 2015 - 06:00:03 PDT
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