[gmx-users] Re: Charges in SW water model

David van der Spoel spoel at xray.bmc.uu.se
Thu Nov 20 13:32:02 CET 2008

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.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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