[gmx-users] free energy: annihilation

David van der Spoel spoel at xray.bmc.uu.se
Sun Aug 27 16:29:07 CEST 2006

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 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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