On Fri, May 23, 2014 at 10:06 AM, Massimiliano Porrini <
m.porrini.iecb.u-bordeaux.fr> wrote:
> On 23 May 2014 14:11, Jason Swails <jason.swails.gmail.com> wrote:
>
> > If performance is really critical to you, you can actually run vacuum
> > dynamics directly on either a NVidia or ATI/AMD GPU (if you have access
> to
> > one) using OpenMM. Their optimized CPU platform may also be a little
> > faster than sander for pure vacuum simulations as well. There is a
> section
> > about OpenMM capabilities in the ParmEd section of the Amber 14 manual,
> and
> > you can find examples here:
> > http://swails.github.io/ParmEd/examples/amber/index.html (use the GB
> > example, but don't pass any value for implicitSolvent).
> >
>
> This is extremely interesting! And I do have access to a Tesla K20 board.
> I am assuming that only in Amber14 this capability is present, therefore it
> might be worth upgrading Amber12 to 14, even though we
> have purchased it very recently (indeed in AmberTools13 ug I did not find
> anything related to OpenMM).
> Useful discussion, as I did not know about the above web page of yours
> either (about ParmEd, I knew only this one
> http://jswails.wikidot.com/parmed#toc7),
> I will have a look at it more carefully to see if I will be able to exploit
> the GPU power for gas phase calculations, thanks.
>
If you are interested in the OpenMM capabilities of ParmEd, you may want to
download the source from Github, as there is more active OpenMM-related
development there than what is available in the AmberTools 14 release.
(Indeed, OpenMM support was added well after AmberTools 13 was released,
so this functionality is AmberTools 14 only).
The main github page for ParmEd is
http://swails.github.io/ParmEd/ (and the
repository is at
http://github.com/swails/ParmEd). Obviously if you wish
to use the ParmEd-OpenMM integration, you will need to install OpenMM as
well (but the performance will be _much_ greater with OpenMM in vacuum than
with sander).
> By no cut-off I assume you refer to an "infinite" cut-off (like the one
> used cut = 1000.0 Angs) and in my runs it resulted that igb=6 is faster
> with Berendsen,
> is slightly faster with Andersen, but slower with Langevin.
>
Yes, infinite cutoff is any cutoff larger than the total system size, at
least as I use the term.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri May 23 2014 - 08:00:02 PDT
