Re: [AMBER] NaN with pmemd.cuda

From: Gould, Ian R <>
Date: Wed, 5 Aug 2015 05:14:27 +0000

Hi Joe,

I have seen this a couple of times myself when GPUšs have been up and
running for several months but not in a reproducible manner.
I usually completely power down the machine that the GPU card is in and
then restart and that has always got rid of the problem.


On 05/08/2015 14:43, "Joseph Baker" <> wrote:

>Hi all,
>I'm running some simulations of dipeptides in water (small systems, about
>1900 atoms total), and in a handful of the simulations am getting NaN's
>the TEMP, Etot and EKtot entries in the output files. I am running Amber
>14, updated as of July 23rd, SPFP. I've seen the error occur on both
>GeForce TITAN Black and GeForce GTX 780 GPUs. I have taken one of the
>simulations and run it a second time using the same random seed value, and
>the NaN error occurs at the exact same simulation step. All other energies
>in the output file are identical between the two simulations.
>I'd appreciate your advice on what might be going on here.
>Joseph Baker, PhD
>Assistant Professor
>Department of Chemistry
>C101 Science Complex
>The College of New Jersey
>Ewing, NJ 08628
>Phone: (609) 771-3173
>AMBER mailing list

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Received on Tue Aug 04 2015 - 22:30:02 PDT
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