[gmx-users] free energy: annihilation

[David van der Spoel]

David Mobley wrote:
> Yuguang reminds me of something else... I just did a bunch of
> hydration free energy calculations for a large set of small molecules.
> These tend to be pretty accurate for stuff that is mostly nonpolar,
> but the larger the charges are, the bigger the deviation from
> experiment can be. In particular, I tested a bunch of different charge
> models; the average error is correlated with the dipole moment, among
> other things. Generally, I would say that the larger your hydration
> free energies are, the worse you will probably do compared to
> experiment, unless you have some way of getting really terrific
> partial charges or something. If DMSO has high partial charges, it
> seems quite possible that the "right" answer for the hydration free
> energy with those partial charges may end up being quite different
> from experiment.
> 
This seems weird, the only physical reason I can think of would be a 
contribution due to depolarization (as in Berendsen's SPC/E model). For 
water this would be roughly 4 kJ/mol. However for DMSO in my case it 
would be less, since it has a high dipole in the gas phase as well. 
Obviously if the model is poor results will be poor.

Could there be some other systematic problem?
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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