I have another follow-up question about faking gas-phase in pmemd (for the
purpose of being able to use CUDA acceleration in case anyone wondered why
one would bother). I can easily change the periodic box size and the
nonbonded cutoff such that I have "full nonbonded" calculations, and I can
also change the PME grid spacing so that the PME portion of the
calculations takes little time (since it is not needed with the full
nonbonded calculations). But what if, as I think may often be the case,
the gas-phase system has a net charge which cannot be reasonably
neutralized? Now the PME will cause problems due to the charged images
surrounding the system.
Is there a way to use pmemd but "fake" the PME? I noticed there is a PME
coefficient, would setting this to 0 effectively case the PME forces to be
null? If that coefficient doesn't do that, is there any way to allow the
PME calculation, but have the forces reduced to 0 or not be applied at all?
Thanks,
~Aron
On Thu, Jan 5, 2012 at 5:15 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> 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
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--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Fri Jan 13 2012 - 21:30:02 PST
