Andreas Kring wrote:
Dear Professor Spoel.
I have a question concerning your article on the SW water model
published in J. Phys. Chem. B, 105, 2618-2626 (2001). I guess the
question is only indirectly related to GROMACS, but I'll post in on the
mailing list since it may be of interest to other GROMACS users as well.
Equation (4) of the paper states that
k_nn = (q_s)^2/alpha_nn,
where nn is either xx, yy or zz. k is the spring constant, q_s is the
charge and alpha is the polarizability. The first line in section 2.2 of
the paper is "After determining the charges and spring constants
corresponding to the polarizabilities...". It seems as if the are too
many unknowns in the equation above, or do I miss something?
If I understand it correctly, the spring constants are determined from
q_s and alpha. But how is the charge determined?
The charges follows from the dipole and the quadrupole of water. We have
three independent variables, and we have three different charges (O,
H, V) and the position of the virtual site, plus the requirement that
the total molecular charge is zero, gives us just enough variable.
Other than that, I would recommend that you look into other polarizable
models as well, because this one is not great.
Hope you can help with this question.
Kind regards
Andreas
--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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