On Wed, Sep 28, 2011 at 11:20 PM, William Cantara <wcantara.gmail.com>wrote:
> Amberites,
>
> I am interested in purchasing a GPU workstation similar to the one
> described
> by Dr Ross Walker at (http://ambermd.org/gpus/index.htm#Hardware). I would
> like to begin doing some PNEB simulations to investigate the optimum
> pathway
> between two conformational states of small RNA stem loops. Will a
> workstation with 2x GTX 580 GPUs be able to run using the multisander
> functionality for a pathway of ~32-64 snapshots in a reasonable amount of
> time? If not, is this something that is being worked on?
>
sander is not GPU-enabled, only pmemd is. NEB and PNEB are not implemented
in pmemd at the moment, so it won't be available on GPUs. To my knowledge,
it's not on the immediate to-do list of things to add to pmemd, either (and
things added to pmemd then have to be ported to the GPU afterwards, which
takes more time). In fact, not all pmemd features are implemented on the
GPU yet (notable things include NMR restraints, for instance).
A multipmemd approach has been implemented in the developmental version of
pmemd both on CPUs and GPUs and will be available for the next Amber release
next year, but each replica will require at least its own GPU (sometimes two
GPUs), so you should keep this in mind when spec-ing out systems.
I would also suggest taking a look at the survey that Ross sent out a short
time ago on this list and filling that out.
HTH,
Jason
> Thank you in advance for any help!
>
> Adieu,
>
> Will Cantara
>
> Graduate Student
> Dept. Mol. & Struct. Biochemistry
> North Carolina State University
>
> Research Project Assistant
> The RNA Institute
> Dept. Biological Sciences
> University at Albany, SUNY
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Sep 28 2011 - 21:30:03 PDT
