Re: [AMBER] pmemd.cuda incomplete output file

From: Andreas Tosstorff <>
Date: Fri, 16 Dec 2016 08:15:59 +0100

Dear Niel,

Thanks for your reply. For both, pmemd and pmemd.cuda, Volume went from
~730000 to ~640000 in 200 ps during equilibration. Pmemd continues working
up to 500 ps as specified, pmemd.cuda does not. No error message to be
found. I also tried pmemd.cuda with an additional 50ps NVT equilibration
before the NPT eq., but no luck there. I also tried the default barostat
instead of Monte Carlo.

Is there anything else I could try?

This is my GPU:

|------------------- GPU DEVICE INFO --------------------
| CUDA Capable Devices Detected: 1
| CUDA Device ID in use: 0
| CUDA Device Name: GeForce GTX TITAN X
| CUDA Device Global Mem Size: 12206 MB
| CUDA Device Num Multiprocessors: 24
| CUDA Device Core Freq: 1.22 GHz

-----Original Message-----
From: Niel Henriksen []
Sent: Friday, December 16, 2016 1:40 AM
To: AMBER Mailing List <>
Subject: Re: [AMBER] pmemd.cuda incomplete output file

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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