Re: [AMBER] error in amber installation

From: Atila Petrosian <atila.petrosian.gmail.com>
Date: Tue, 5 May 2015 10:38:11 +0430

Dear Jason

Very thanks for your quick answers and guidance.

I have Amber 11 and AmberTools14. If I want to run MD on cpu, which of
following option is suitable to run MD faster?

sander.MPI
or
pmemd.

Excuse me for many question.

--
Atila
On Mon, May 4, 2015 at 10:33 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Mon, May 4, 2015 at 1:51 PM, Atila Petrosian <atila.petrosian.gmail.com
> >
> wrote:
>
> > Dear Jason
> >
> > Thanks for your answer.
> >
> > Is pmemd related to GPU, only?
> >
>
> ​pmemd runs on CPUs, too.  But pmemd on the GPU is *much* faster than pmemd
> on CPUs for most GPUs (see​
>  http://ambermd.org/gpus/benchmarks.htm#Benchmarks
> ​ for detailed timings).​
>
> If I install ambertools on cpu, can I install pmemd? or not?
> >
>
> If you want pmemd from Amber 11, it can run on CPUs, but not GPUs.  But
> pmemd from Amber 11 can be a challenge to compile.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Mon May 04 2015 - 23:30:02 PDT