Re: [AMBER] Updates for PBSA energy calculations

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Tue, 29 Sep 2015 09:57:05 -0700

A CUDA version of PBSA is in the planning for next year's release. I
think this is probably more useful for many Amber users.

Ray

--
Ray Luo, Ph.D.
Professor
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Mon, Sep 28, 2015 at 10:07 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Mon, Sep 28, 2015 at 7:17 PM, Christina Berti <cberti.purdue.edu> wrote:
>
>> Hello,
>>
>> To my knowledge, neither sander.MPI nor pmemd.MPI are implementable when
>> performing PBSA energy calculations in sander. I was wondering if users
>> should expect an update in the near future. Thank you.
>>
>
> No.  pmemd has never (and likely will never) support PBSA.  sander only
> links to the serial versions of PBSA and I know of no plan to extend this
> to the parallel version.
>
> If you want to run parallel PB calculations, check out the pbsa.MPI
> executable.  MMPBSA.py.MPI can also parallelize MM/PBSA calculations.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Tue Sep 29 2015 - 10:00:03 PDT