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

From: David A Case <>
Date: Wed, 17 Jun 2015 08:23:42 -0600

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"

Thanks for the report....regards...dac

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Received on Wed Jun 17 2015 - 07:30:04 PDT
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