AMBER Archive (2009)

Subject: [AMBER] Solvation potential and free energies

From: guardiani_at_fi.infn.it
Date: Thu Feb 05 2009 - 06:27:21 CST

Dear Amber experts,

I am currently performing REMD simulations
using the Generalized Born solvent model
(igb=7). Everything is working very well,
and I have just a little theoretical question.

In the Amber9 manual I read that, in order to
attain the GB/surface-area force field, it is
sufficient to add to the vacuum force field
the term (Eq 5.3 of Amber9 Manual):

\sum_{ij}\frac{q_{i}q_{j}}{f^{gb}(R_{ij})} + \sigma*A

This expression, however, is different from the
one that can be derived from Equations 2 and 3 of
your paper J. Phys. Chem. B, Vol 104, No 15, 2000.

As I understand, Equation 2 represents the Coulomb
contribution in a protein-like environment, and this
term corresponds to the Coulomb contribution in the
Amber vacuum force-field. In order to account for
the solvation effects, it is then necessary to add
Equation 3:

-\frac{1}{2}(\frac{1}{\epsilon_{p}} - \frac{1}{\epsilon_{w}})
\sum_{ij}\frac{q_{i}q_{j}}{f^{gb}(R_{ij})}

This expression, however, is not the same as
equation Eq 5.3 of Amber9 Manual due to the
presence of the factor
-\frac{1}{2}(\frac{1}{\epsilon_{p}} - \frac{1}{\epsilon_{w}})

Could you please explain the reason for this difference ?

In general, I noticed that in all papers about continuum
solvent models the goal is to compute the electrostatic
component of the solvation free energy. No mention is made
of potential energy. Could you briefly explain (or refer me
to the appropriate literature) the relation between solvation
free energy and solvation potential energy ?

Lots of thanks for your help.

Best regards,

Carlo Guardiani

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