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

From: Patrick von Glehn <>
Date: Wed, 22 Aug 2012 15:28:50 +0100

Hi Scott,

Thanks for your reply.

Do you have reason to believe that the new patch will resolve this
error? Were you able to reproduce the error with an unpatched version
of amber? Also, forgive my ignorance, but what does TOT mean?

What sort of timescale are we talking about here for the new patch
release? Days/weeks/months? I am very keen to get my GPU simulations

All the best,

On 21 August 2012 03:35, Scott Le Grand <> wrote:
> 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
>> _______________________________________________
>> AMBER mailing list
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Received on Wed Aug 22 2012 - 07:30:04 PDT
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