Re: [AMBER] Calculation halted while running simulation

From: David A Case <>
Date: Fri, 4 Dec 2020 08:18:32 -0500

On Fri, Dec 04, 2020, angad sharma wrote:

>I am running a simulation on dsDNA. It runs well till minimization and
>heating but as it starts for the equilibration process within a minute it
>stops by showing the following error:-

I guess I will push back a little here. The error message you quote
(reproduced below) is about as specific and detailed a message as you
will ever get from Amber. It lists two things you can check (is
your energy getting very high, is the density changing by a lot?)

It also suggests two things to try: (a) restart the calculation,
perhaps several times; (b) use the CPU code until you get closer to a
converged density. [Personally, I tend to use the latter approach.]

Did you try any of these suggestions? Note also that it can be
dangerous to both heat the system and be running constant pressure
(allowing the density to change) at the same time.

Some good advice about equilibration is given by Roe and Brooks,
J. Chem. Phys. 153, 054123 (2020); doi: 10.1063/5.0013849. Note that
final density equilibration only comes at the last step, and that most
earlier steps use a 1 fs time step. It is certainly worth trying some
of the ideas given in this paper if you are having troubles with system

...good luck....dac

>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]
> The GPU code does not automatically reorganize grid cells and thus you
>will need to restart the calculation from the previous restart file.
>This will generate new grid cells and allow the calculation to continue.
>It 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.

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Received on Fri Dec 04 2020 - 05:30:03 PST
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