AMBER Archive (2003)

Subject: Re: solvent free energy, GB

From: David A. Case (case_at_scripps.edu)
Date: Thu Jan 16 2003 - 18:25:16 CST

On Thu, Jan 16, 2003, Robert G. Endres wrote:
>
> Correct me if I am wrong: the GB is used to calculate the contributions to
> the free energy of solvation for charged atoms, the "surften" is the
> contribution from uncharged atoms?

Not really: GB estimates the "electrostatic contribution" to solvation; even
uncharged atoms contribute, at least indirectly, by exclision of water from
where they are. Hence, the GB term is a property of the entire molecule.

The SA term estimates the "non-electrostatic contribution" (i.e. everything
else). Even a rare-gas atom has a non-zero solvation free energy, and it is
the goal of SA to estimate this part. As with GB, both charged and
non-charged atoms contribute.

There can be cases where the *change* in SA over the course of the trajectory
(or over the range of conformations of interest) is expected to be small.
In such circumstances, one could justify omitting it, since only differences
in energy are generally of interest. But omitting the SA term for this reason
is an approximation, the accuracy of which would vary from one application to
the next.

..hope this helps...dac

p.s I think the Sitkoff et al paper contains one of the clearer explications
of all these ideas:

%A D. Sitkoff
%A K.A. Sharp
%A B. Honig
%T Accurate calculation of hydration free energies using macroscopic solvent
models
%J J. Phys. Chem.
%V 98
%P 1978-1988
%D 1994
%K parse 

-- 

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