AMBER Archive (2006)

Subject: Re: AMBER: a quetion

From: darden (darden_at_gamera.niehs.nih.gov)
Date: Mon Apr 24 2006 - 09:57:59 CDT

In amber the electrostatic forces are treated both in real and k space.
The vdw forces are only done in real space. It is possible to also treat
them by ewald methods, but we don't due to the more complex mixing rules
in vdw. Basically, any method that attempts to accelerate vdw tries to
reduce the problem to something looking like coulomb's law so that you can
use the fast methods developed for that case. But vdw pair interactions
usually look different. It can be done for the Lorentz-Berthelot rules
used by the amber force field---but the result is usually not worth the
effort compared to other simpler strategies such as long-range analytic
correction which we do use.
So the cutoff refers to the direct space ewald (pme) treatment forc
electrostatics and also for vdw. Electrostatics are supplemented by a
k-space treatment using pme. Vdw are supplemented by a long-range
continuum correction
hope this helps
tom d

On Mon, 24 Apr 2006, german wrote:

> Dear amber users,
>
> I had a problem with my e-mail and so I am repeating the following questtion,
>
> I'd like to know if anyone knows, how the PME works..I have a technical
> question regarding PME...
> Is the value of CUT the cut off value only for VdW forces in the direct (r)
> space? and are only the electrostatic forces (EF) treating in the k space? or
> are VdW and EF cutoff in the r space and some contribution of the EF is
> considered in the k space?
>
> Thanks in advance...
>
> German...
>
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