Thank you very much.
Sajeewa
On Fri, Oct 5, 2012 at 10:27 AM, Jason Swails <jason.swails.gmail.com>wrote:
> On Fri, Oct 5, 2012 at 7:48 AM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > pmemd can be used on more cores than sander for GB calculations. not just
> > better scaling, but sander has hard limits of # cores for GB (1 per
> > residue, I think).
> >
>
> True, sander has that limit since the bond/angle/dihedral workload is
> broken up by residue, but pmemd has a similar, but slightly smaller, limit
> in place (10+ atoms per core or pmemd will complain). The main GB loop is
> still parallelized exactly the same way in both programs, and so they even
> scale similarly.
>
> In fact, I think the *fastest* GB routines in Amber are in NAB*, since it
> has a nonbonded pairlist for GB (although I can't speak on the parallel
> scaling).
>
> All the best,
> Jason
>
> *Fastest CPU routines
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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>
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Received on Fri Oct 05 2012 - 08:00:03 PDT
