Re: [AMBER] transition metal system works on pmemd crashes on pmemd.cuda

From: Scott Le Grand <>
Date: Mon, 20 Aug 2012 19:35:09 -0700

Works in TOT at my end... Patch coming out shortly...

On Mon, Aug 20, 2012 at 4:37 PM, Patrick von Glehn <> wrote:

> Dear Amber mailing list,
> I have been successfully running molecular dynamics simulations on
> vitamin B12 (a hexacoordinate cobalt complex) systems using pmemd on
> CPUs for some time.
> When I tried to rerun exactly the same simulations on pmemd.cuda.SPDP
> (on NVIDIA Tesla M2090 GPUs using amber 12 with bugfixes 1 to 7
> applied) the system blows up with the following error message:
> ERROR: max pairlist cutoff must be less than unit cell max sphere radius!
> This occurs after a few steps (usually 1 or 2).
> In the zipped folder attached I have included all of the necessary
> .lib .frcmod and .pdb files and a tleap script to generate a simple
> solvated hexacoordinate B12 system.
> I have also attached the input and output files and submission scripts
> used to run minimizations and short unrestrained MD simulations
> (successful on pmemd and unsuccessful on pmemd.cuda.SPDP).
> I created the .lib and .frcmod files myself based on parameters in the
> literature. To see if the problem was with my parameters I tried to
> simulate a solvated heme molecule (a very similar system to B12) using
> the parameters from the Bryce group database
> (which by the way
> appear to be missing nonbonded parameters for a few atom types).
> Exactly the same error occurred with heme as with B12
> I found that if I removed the cobalt atom entirely the problem
> disappears. The problem also disappears if I remove most of the bonds
> to the cobalt atom.
> Many thanks in advance to anyone who can shed some light on this.
> Patrick von Glehn
> PhD student
> Harvey and Mulholland groups
> University of Bristol
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Received on Mon Aug 20 2012 - 20:00:04 PDT
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