On Thu, Sep 29, 2011 at 12:01 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi William,
>
> > 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?
>
> What is meant by the P in PNEB? - AMBER supports Nudged Elastic Band
> simulations right now but only on CPUs through the Sander package. While I
> would ultimately like to port the NEB code to GPUs it is a way down the
> priority list behind things like umbrella sampling restraints,
> Thermodynamic
> integration etc.
>
I think the P here means "Partial". It's part of Christina's (relatively)
new re-implementation of NEB in sander. Someone in Carlos's group can
correct me if I'm wrong here. To my limited knowledge of NEB, I think it's
just an approach that doesn't need to replicate the entire system, but
merely subsections of the system (like, for instance, a disordered loop or
something). I think that means it'll require fewer beads, and probably
other benefits I'm unaware of.
Of course this analysis comes based on what I think I remember from one (or
some?) of Christina's talks at the developer meeting(s) and stuff I think I
may have seen in the manual about it.
(You can probably gauge pretty accurately the conviction I have here :) ).
All the best,
Jason
--
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 - 21:30:04 PDT
