Re: [AMBER] Res-Res energy shows different value with or without explicit solvent

From: Jason Swails <>
Date: Tue, 19 Nov 2013 07:53:48 -0500

On Tue, 2013-11-19 at 21:06 +0900, kurisaki wrote:
> Dear Amber Users,
> I found that Res-Res energy shows different value
> With or without explicit solvent, i.e.,
> With solvent
> TDC 79-> 79 0.000 -1.567 -5.462 0.000 0.000
> Without solvent
> TDC 79-> 79 0.000 -1.346 -5.709 0.000 0.000
> I thought that res-res energy meant direct non-bonded interaction energy
> between the two residues, but does it include energetic contribution from
> the other all residues?

The direct-space electrostatic term in PME is screened. The
electrostatic term in implicit solvent is not. The direct-space
screening in PME is removed in the reciprocal space part of the PME
calculation, and this part is _not_ decomposable. As a result, I think
it is likely ignored.

The screening (which is caused by an artificial neutralizing charge
distribution centered on each particle) is part of the Ewald technique
for computing electrostatic energies in an infinitely periodic system.
The Allen and Tildesley book has a nice description of it (as do several
other general computational chemistry books).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Nov 19 2013 - 05:00:02 PST
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