Re: [AMBER] pmemd.cuda incomplete output file

From: Niel Henriksen <>
Date: Thu, 15 Dec 2016 16:39:56 -0800

On Thu, Dec 15, 2016 at 1:31 PM, Andreas Tosstorff <> wrote:

> Hi all,
> I ran the same job with pmemd instead of pmemd.CUDA and it worked just
> fine. Any suggestions how I could make it run on pmemd.CUDA?
Hi Andreas,

Just a guess here, but is there any chance the volume is changing
significantly during equilibration? If that is the case, you might see the
error message I've copied below. Sometimes I've missed that message if
stdout/stderr is redirected in a non-standard way (ie, batch/queue system).


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 Thu Dec 15 2016 - 17:00:03 PST
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