[AMBER] NaN with pmemd.cuda

From: Joseph Baker <bakerj.tcnj.edu>
Date: Wed, 5 Aug 2015 00:43:22 -0400

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 for
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
Web: http://bakerj.pages.tcnj.edu/
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Received on Tue Aug 04 2015 - 22:00:02 PDT
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