AMBER Archive (2003)

Subject: Re: PME

From: darden (darden_at_gamera.niehs.nih.gov)
Date: Wed Jun 11 2003 - 09:33:12 CDT

Dear Yuguang
Ordinarily the ewald sum consists of a direct sum, a reciprocal sum and a
self-term. This is all you need if your system is ions or other point
charges. In molecular systems force fields such as amber don't calculate
electrostatic interactions between certain close neighbors on the
same molecule e.g. bonded pairs. To be more explicit an oxygen and
hydrogen on a water are not supposed to feel each other. The direct sum
contribution for the interaction between these can be masked out, i.e.
that hydrogen is not in the nonbond list of the oxygen of the water in
question. However the reciprocal sum contribution of that pair is
calculated. Since this is not a sum of pairs calculation (that would make
it necessarily order n^2 where n is number of atoms) we can't mask out
these pair contributions. So we calculate them separately in the ajustment
term and remove them from the ewald sum. The number is large since nearby
pairs interact strongly, even in the reciprocal sum.

Hope this helps
Tom Darden

On Wed, 11 Jun 2003, Yuguang Mu wrote:

> What is the meaning of adjustment energy in PME of AMBER
> ANd this term seems quite large compared with other terms,
> like Edir, Rrec, Eself . How comes ?
>
> Dr. Yuguang Mu
> Institute for Physical and Theoretical Chemistry
> J.W. Goethe University Frankfurt am Main
> Marie Curie Str. 11
> 60439 Frankfurt/Main, Germany
> Tel: +49-(0)69-798-29711
>
>