Hi again. Many thanks to all for caring about this issue.
Stephan, I have tried to make the pull with a force constant equal to zero
and still had the same issue, so I do not think that the speed of the pull
is the issue.
Additionaly, Dr. Roitberg managed to help me out and finally the pull
worked. He suggested to use group selections excluding hydrogen atoms and
this worked just fine.
Many thanks!
Regards
Gerardo Zerbetto De Palma
El vie., 15 mar. 2019 a las 11:15, Stephan Schott (<schottve.hhu.de>)
escribió:
> Hi,
> I don't think it is necessarily related. You get this kind of error when
> you lose track of atoms for a certain reason. In this case it looks like
> you might be pulling too fast? (13A in 100 ps, which would be ~46 km/hr?).
> Have you tried with lower velocities? Try doing the simulation at about 1
> A/ns and tell us if then it works. Also please tell us what version of
> AMBER you are using, with what patches and make sure you start from an
> "equilibrated" structure. If it is in anyway related to the COM restraint
> issues, I know that a patch from Charles Lin is on the way, so it should be
> working in the next days.
> Cheers,
>
> El mié., 13 mar. 2019 a las 21:48, Pratul Agarwal (<pratul.agarwal-lab.org
> >)
> escribió:
>
> > This sounds similar to the issues being discussed here:
> > http://archive.ambermd.org/201903/0095.html
> > or
> > http://archive.ambermd.org/201903/0056.html?
> >
> > Pratul K. Agarwal, Ph.D.
> > (Editorial Board Member: PLoS ONE, Microbial Cell Factories)
> > Web: http://www.agarwal-lab.org/
> >
> >
> > On 3/13/2019 1:21 PM, Gerardo Zerbetto De Palma wrote:
> >
> > Hello! First time in this mailing list.
> > I am having an issue making a pull between two centers of mass of two
> atom
> > groups, using pmemd.cuda. The stdout reads:
> >
> > cudaMemcpy GpuBuffer::Download failed an illegal memory access was
> > encountered
> >
> > When I run this on sander, it works just fine, so I think the system is
> not
> > blowing up.
> > I have also tried:
> > - running a plain simple simulation (not pulling) with pmemd.cuda and in
> > also worked just fine.
> > - running a simulation pulling from 2 individual atoms (not center of
> mass)
> > and it also worked fine.
> >
> > I am attaching the mdin, restraint and output files for the center of
> mass
> > pulling.
> > Thanks a lot.
> > Best regards!
> >
> > Gerardo Zerbetto De Palma
> > Universidad de Buenos Aires
> >
> >
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org<mailto:AMBER.ambermd.org>
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Stephan Schott Verdugo
> Biochemist
>
> Heinrich-Heine-Universitaet Duesseldorf
> Institut fuer Pharm. und Med. Chemie
> Universitaetsstr. 1
> 40225 Duesseldorf
> Germany
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Mar 15 2019 - 08:30:03 PDT
