In answer to your original question, yes, pmemd and pmemd.cuda from Amber
12 supports REMD simulations through a "multi-pmemd" setup just like sander.
Unlike sander, however, pmemd.MPI will not run with a single thread, since
that code path is optimized to run in parallel. Therefore, you will need
to use at least 2 processors for each replica in pmemd REMD simulations.
The GPU version, on the other hand, will run REMD with 1 GPU per replica.
HTH,
Jason
On Tue, Jan 22, 2013 at 5:21 AM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
> I tried to run mpirun pmemd.MPI -ng 4 -groupfile
> I get following error msg as pointed out by others before: *MPI version of
> PMEMD must be used with 2 or more processors*!
>
> However, when I am able to successfully run
> mpirun sander.MPI -ng 4 -groupfile
> mpirun pmemd.MPI -O -i input file -c
>
> Kindly help!
> Regards,
> Neha
>
>
> On 22 January 2013 17:20, Neha Gandhi <n.gandhiau.gmail.com> wrote:
>
> > Dear List,
> >
> > I might have missed out on mailing list. I was wondering if there is
> multi
> > pmemd functionality in amber 12 which might allow REMD simulations? I am
> > not sure either about the implementation of 1-D temperature REMD using
> > AMBER 12 on GPU/CPU ? How do you run such simulations?
> >
> > Many thanks,
> > Neha
> >
> > --
> > Regards,
> > Dr. Neha S. Gandhi,
> > Curtin Research Fellow,
> > School of Biomedical Sciences,
> > Curtin University,
> > Perth GPO U1987
> > Australia
> > LinkedIn
> > Research Gate
> >
>
>
>
> --
> Regards,
> Dr. Neha S. Gandhi,
> Curtin Research Fellow,
> School of Biomedical Sciences,
> Curtin University,
> Perth GPO U1987
> Australia
> LinkedIn
> Research Gate
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Jan 22 2013 - 05:00:03 PST
