AMBER Archive (2006)

Subject: Re: AMBER: TI tutorial

From: David A. Case (case_at_scripps.edu)
Date: Tue Aug 15 2006 - 18:34:58 CDT

On Tue, Aug 15, 2006, Mingfeng Yang wrote:

> On the homepage of Amber, in the tutorial of Thermodynamic Integration
> written by Dr. David Case, there is a sentence like "I have also used only
> three values of *clambda*, based on experience that charging free energies
> are very smooth functions of *clambda*." Is there any references which I
> can cite to prove this sentence is correct?
>

Here are a few papers that investigate this issue in the context of
explicit solvent MD simulations:

%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

%A T. Simonson
%A J. Carlsson
%A D.A. Case
%T Proton binding to proteins: pKa calculations with explicit and implicit
%solvent models
%J J. Am. Chem. Soc.
%V 126
%P 4167-4180
%D 2004

%A M.R. Shirts
%A J.W. Pitera
%A W.C. Swope
%A V.S. Pande
%T Extremely precise free energy calculations of amino acid side chain
analogs: Comparison of common molecular mechanics force fields for proteins
%J J. Chem. Phys.
%V 119
%P 5740-5761
%D 2003

The "smoothness" of charging free energies is basic to a great many other
calculations as well, including almost everything that Warshel has done; you
might check out this:

%A A. Warshel
%A J. Aqvist
%T Electrostatic energy and macromolecular function
%J Ann. Rev. Biophys. Biophys. Chem.
%V 20
%P 267-298
%D 1991

...dac
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