Hi Aron,
AMBER 12 will support 'real' <cough> gas phase simulations in pmemd both on
CPU and GPU.
All the best
Ross
> -----Original Message-----
> From: Aron Broom [mailto:broomsday.gmail.com]
> Sent: Thursday, January 05, 2012 1:55 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Gas Phase Simulations in PMEMD
>
> Ahh, I was confused, I thought from my initial reading that nfft was
> the
> grid dimension (A,B,C). That will work perfectly then.
>
> Thank you.
>
> ~Aron
>
> On Thu, Jan 5, 2012 at 4:29 PM, George M Giambasu
> <giambasu.gmail.com>wrote:
>
> > Look for nfft1,2,3 in section 2.7.2 of
> > http://ambermd.org/doc11/Amber11.pdf
> >
> > george
> >
> > > While the above approach should work, it means that you are doing a
> lot
> > of
> > > PME calculations (calculating the grid and such) that really aren't
> > useful
> > > (since most of that space is a vacuum). I know that in NAMD for
> instance
> > > one can specify the PME grid spacing to be different than the
> standard 1
> > > angstrom. This would seem to be the best solution for this
> problem, to
> > > have a large periodic box and use PME, but to have the PME spacing
> large
> > > enough that there is really only one grid point and also have the
> > > electrostatic cutoff be high enough that full electrostatics are
> always
> > > performed such that PME is never actually used. Is there a way to
> > specify
> > > the PME grid spacing in AMBER? I didn't see it in the manual
> anywhere.
> > >
> > > Thanks,
> > >
> > > ~Aron
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jan 05 2012 - 14:30:03 PST
