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From: darden <darden.gamera.niehs.nih.gov>

Date: Wed, 11 Jun 2003 09:33:12 -0500 (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
*

*>
*

*>
*

Received on Wed Jun 11 2003 - 15:53:01 PDT

Date: Wed, 11 Jun 2003 09:33:12 -0500 (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:

Received on Wed Jun 11 2003 - 15:53:01 PDT

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