# Re: [AMBER] Simulations without PME

From: Tom Kurtzman <simpleliquid.gmail.com>
Date: Tue, 6 Aug 2019 12:03:27 -0400

Hi Dave and Bill, thanks for the responses. Much appreciated.

This for a periodic system but for troubleshooting GIST calculations which
calculates electrostatics explicitly for the entire system (minimum image
convention but no longer range contributions) so I wanted to run MD (on a
neutral system) with electrostatics calculated explicitly over all minimum
image pairs but with no long-range corrections for which this would be
exact.

Since erfc(\alpha r) is not equal to one, the short range part for PME is
not identical to this (within the cutoff).

I'll check the manual on eedmeth=4 and source dive for specifics.

Thanks again,

Tom

On Mon, Aug 5, 2019 at 9:43 PM Bill Ross <ross.cgl.ucsf.edu> wrote:

> For non-periodic calcs, running in vacuum with a huge cutoff would do
> it, be sure you are ready to defend it and maybe have a big drop of
> water going on.
>
> Bill
>
> On 8/5/19 6:18 PM, David Case wrote:
> > On Mon, Aug 05, 2019, Tom Kurtzman wrote:
> >
> >> Is it currently possible to run simulations without using particle mesh
> >> ewald at all? (using full pairwise calculations of electrostatic
> >> energies?). With no long range corrections whatsoever?
> > Are you thinking of a periodic or non-periodic calculation?
> >
> > For periodic calculations, you can set eedmeth=4: this will compute
> > pairwise electrostatics out to cut, and nothing beyond that. There will
> > be no reciprocal calculation done. (See the manual for details.)
> >
> > However, the maximum value for cut+skinnb is still half the box length.
> > There is no code in Amber that knows how to compute atom pairs beyond
> > the minimum-image convention.
> >> The Amber Manual suggests setting the PME cutoff very high.
> > Can you say exactly where this suggestion is? Sounds nonsensical to me,
> > unless you are dealing with a non-periodic simulation. But I could be
> > missing something about why this (seemingly odd) suggestion was made.
> >
> > ....dac
> >
> > p.s.: just so it is clear to everyone: using eedmeth=4 is *not*
> > recommended for any type of routine use, and will generally give very
> > bad results if you just turn that option on.
> >
> > _______________________________________________
> > 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
>

--
************************************************
Tom Kurtzman, Ph.D.
Associate Professor
Department of Chemistry
Lehman College, CUNY
250 Bedford Park Blvd. West
Bronx, New York 10468
718-960-8832
http://www.lehman.edu/faculty/tkurtzman/
<http://www.lehman.edu/faculty/tkurtzman/index.html>
************************************************
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

Received on Tue Aug 06 2019 - 09:30:02 PDT
Custom Search