AMBER Archive (2008)

Subject: Re: AMBER: Hydration free energies of charged ions using PME

From: David A. Case (
Date: Wed May 28 2008 - 11:51:26 CDT

On Wed, May 28, 2008, Markus Kaukonen wrote:
> Finally, could somebody point out a publication were
> standard-periodic-AMBER would have been used to calculate absolute
> free energies for charged systems?

The standard reference is here:

%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

Tom Darden may want to comment the individual terms (with all kinds of
confusing terminology!) that you mention. A lot of the confusion comes from
the difference between how Monte Carlo simulations are coded, compared to MD


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