Re: [AMBER] pmemd.cuda incomplete output file

From: Niel Henriksen <>
Date: Thu, 22 Dec 2016 07:58:17 -0800

On Thu, Dec 22, 2016 at 7:39 AM, Andreas Tosstorff <> wrote:

> I finally was able to get at least an error message for my problem by
> running the job directly from the command line:
> ERROR: Calculation halted. Periodic box dimensions have changed too much
> from their initial values.

Ah, ok this is what I suspected.

> So far I tried a 50ps NVT eq before the NPT eq. Do you think a longer NVT
> eq
> could help here?

No. This is simply a limitation of pmemd.cuda (ie, "The GPU code does not
automatically reorganize grid cells"). The problem will show up anytime
the box
size changes significantly, and no amount of constant volume simulation will
prevent box size changes during subsequent constant pressure simulation if
the density starts off wrong.

A few suggestions:
1) just restart your simulation as the error message suggests.
2) use pmemd/pmemd.MPI to do your initial NPT equilibration
3) Run many short NPT equilibrations in a row to force recalculation of
grid cells.

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Received on Thu Dec 22 2016 - 08:00:02 PST
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