Re: AMBER: Ewald calculation using PME for charged system

From: David A. Case <>
Date: Wed, 10 Mar 2004 00:11:54 -0800

On Wed, Mar 10, 2004, Wayne Dawson wrote:
> I doubt that the authors (if they know any physics and chemistry at
> all), would purposely build a __whole PERIODIC system__ that had a net
> excess of charge. Yes the protein may have had a net
> positive/negative charge, or the system could contain "extra ions",
> but these were surely balanced by an equal number of oppositely
> charged ions to make the __SYSTEM__ neutral, although the authors may
> not have said so explicitly.

This is not correct. There are lots of simulations in which the system
has a net charge, which is implicitly balanced by a neutralizing plasma.
There is no need to have an equal number of oppositely charged [explict]

As an example, one could not easily do charging free energies (such as redox
or pKa calculations) using pme if there was a real restriction to uncharged
systems. Yet such calculations are quite common, and give good results.
You might want to look at the following:

%A T. Darden
%A D. Pearlman
%A L.G. Pedersen
%T Ionic charging free energies: Spherical versus periodic boundary
%J J. Chem. Phys.
%V 109
%P 10921-10935
%D 1998

%A T. Simonson
%T Gaussian fluctuations and linear response in an electron transfer protein
%J Proc. Natl. Acad. Sci. USA
%V 99
%P 6544-6549
%D 2002

....hope this helps...dac
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Received on Wed Mar 10 2004 - 08:53:01 PST
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