Re: [AMBER] NMR restraints with pmemd.cuda problem

From: Ross Walker <>
Date: Wed, 17 Jun 2015 08:00:52 -0700

There is most likely a hard limit in the code - we can take a look but can you send me (by private mail if need be) the necessary input files to reproduce this failure.

Thank you.

All the best

> On Jun 17, 2015, at 7:23 AM, David A Case <> wrote:
> On Tue, Jun 16, 2015, Miroslav Krepl wrote:
>> since the com restraints were recently implemented into the GPU version,
>> I have tried to run a simple explicit solvent simulations of some
>> proteins from the PDB database while using the experimental NMR
>> restraints (nmropt=1; distance based restraints, about 2000 of them).
> Certainly sounds like a bug.
>> 5. It seems that the number of NMR restraints might be the key. I have
>> tried reducing the number to only few (1, 4 etc.) and it appreared to be
>> working. However, I was unable to determine the exact number of
>> restraints beyond which it starts to crash.
> I'm guessing it is more that some nmr restraints make use of the COM facility
> and some don't. Can you see if the crashes are related to the presence or
> absence of restraints with iat=-1?
> But we shouldn't dump any more debugging on you, since you've already done a
> lot. I'm travelling right now, but any developer with access to a GPU, (and
> with knowledge about the GPU code!) should be able to test this way:
> cd $AMBERHOME/test/nmr
> export TESTsander="../../bin/pmemd.cuda"
> ./Run.nmr
> Thanks for the report....regards...dac
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Received on Wed Jun 17 2015 - 08:30:02 PDT
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