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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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