You must purchase pmemd.cuda, but it comes as a package with the parallel
CPU pmemd. The analysis tools and the sander engine are what you get with
AmberTools. If you want to run on small numbers of processors, you may be
able to use the mdgx engine also distributed with AmberTools for your
purposes; its speed is comparable to pmemd on similar numbers of cores, but
the output does not exactly conform to sander and it doesn't do everything
sander does. If you need perfectly reproducible results, pmemd CPU is
designed to match sander to machine precision and sander is the gold
standard. pmemd.cuda is somewhat faster than either sander or CPU pmemd.
Dave
On Mon, Apr 16, 2018 at 2:13 PM, Atila Petrosian <atila.petrosian.gmail.com>
wrote:
> Dear Setyanto,
>
> Thanks for answer.
>
> How to install AmberTools17 to use pmemd.cuda under gpu?
>
> Is pmemd.cuda faster than sander?
>
> Best,
> Atila
>
> On Mon, Apr 16, 2018 at 2:52 AM, Setyanto Md <stwahyudi.md.gmail.com>
> wrote:
>
> > Dear Atika Petrosian,
> >
> > You can use pmemd.cuda instead of sander, to do long simulation.
> >
> > Regards,
> > Setyanto
> >
> > Pada tanggal 15 Apr 2018 12.58 PM, "Atila Petrosian" <
> > atila.petrosian.gmail.com> menulis:
> >
> > Dear Scott,
> > Thanks for your answer.
> >
> > On Sun, Apr 15, 2018 at 1:36 AM, Scott Brozell <sbrozell.rci.rutgers.edu
> >
> > wrote:
> >
> > > Hi,
> > >
> > > On Sat, Apr 14, 2018 at 08:29:32PM +0430, Atila Petrosian wrote:
> > > > Which version of amber has free module of sander?
> > > >
> > > > Is this version GPU-supported?
> > >
> > > All of AmberTools is free and it contains sander.
> > > AmberTools17 is available for download at the Amber web site.
> > > Amber18 which includes AmberTools18 will be released soon.
> > >
> > > sander is not GPU-supported.
> > >
> > >
> >
> > > I have many molecular systems to do md simulation with long simulation
> > > time. Thus, I need to do them using GPU.
> > >
> > > Isn't there an alternative for sander under GPU?
> > >
> > >
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Received on Mon Apr 16 2018 - 12:00:03 PDT
