[gmx-users] Ion Polarizability (Shell Model)

David van der Spoel spoel at xray.bmc.uu.se
Fri Dec 19 08:15:51 CET 2008

Eric Shamay wrote:
> In researching the shell model used to create "polarizable" ions I came 
> across several of the references of the drude oscillator approach and 
> the papers of van der Spoel (for the SW water model) and Roux (for the 
> parameters of the halides and alkalis). However, perhaps due to my own 
> oversight, I did not walk away from those publications having a firm 
> understanding of just how one goes about developing the parameters 
> necessary to implement the shell model, even for simple monovalent ions 
> (i.e. sodium).
> I am attempting to simulate an aqueous sodium chloride system using a 
> polarizable (shell) model for the individual sodium and chloride ions, 
> but eventually I will also need data for nitrate and sulfate ions. Is 
> there a more clear reference that illustrates the process (or lists the 
> results) of developing the parameters (force constant [k], charge of the 
> shell particle [q_s], etc.) for using the shell model? I'd like to be 
> able to come up with my own values, but a published set will work as 
> well. As a side note, I'm coming from having used the amber 
> point-polarizable model that assigns an isotropic alpha to each 
> particle. I can calculate the polarizability tensor using DFT methods, 
> but still don't know how to translate that into a force constant or 
> shell-particle charge.

The equations are in the SW paper. However in case of a singly charged 
atom like Na+ you have one extra degree of freedom. In case of molecular 
ions you can use e.g. RESP calculations to get the partial charges and 
use these to determine the spring constant.

Note that you will also need to update Van der Waals parameters.

> thank you,
> ~Eric Shamay
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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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