Re: [AMBER] Simulation run issue

From: David Case <>
Date: Mon, 18 Nov 2019 12:27:52 +0000

On Mon, Nov 18, 2019, Sayan Poddar wrote:
>*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. [Although this error can also occur if the
>simulation has blown up for some reason]

This message should spur you to look at the density variations you are
seeing. The message indicates a guess that you started from a density a
long way from equilibrium: is this indeed the case?

>may be necessary to repeat
>this restarting multiple times if your system is a long way from an
>equilibrated density. Alternatively you can run with the CPU code until
>the density has converged and then switch back to the GPU code.*

Did you try either of the suggestions above?

>I have never faced this issue before. However this problem is being shown
>by only two glycans. My other glycans run perfectly on Amber18.

Try to see what might be different between the ones that work and the
ones that don't. Concentrate on any constant pressure steps where the
volume and the density of the system are changing.


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Received on Mon Nov 18 2019 - 04:30:02 PST
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