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

From: Miroslav Krepl <krepl.seznam.cz>
Date: Wed, 17 Jun 2015 20:50:13 +0200

Dear all,

I sent the topology, CDF restart file, Amber input and the NMR
restraints of the problematic system (although no other system I tested
so far worked on GPU either) in the attachment.

Some more debug I forgot to mention:

I tried including/exluding the COM restraints (iat=-1), but I could find
no relation. With very few restraints it worked and it did not matter
whether they were COM or normal. With more restraints, it failed.

However, I did indeed observe that the Ile, Leu and Phe side-chain atoms
(i.e. those that are usually heavy on the COM definition) were the first
to blow up with the first integration step. But I am not sure whether
this is consequential. It could be random.

Thank you!

Best wishes,

Miroslav Krepl

On Wed, 2015-06-17 at 08:00 -0700, Ross Walker wrote:
> 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
> Ross
>
> > On Jun 17, 2015, at 7:23 AM, David A Case <case.biomaps.rutgers.edu> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Wed Jun 17 2015 - 12:30:02 PDT
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