[gmx-developers] Shell polarization

David van der Spoel spoel at xray.bmc.uu.se
Tue May 13 07:54:23 CEST 2008

Juan S. Medina Alvarez wrote:
> Hello,
>  I'm working with a polarizable model of Water (TTM2.1F) and I try to 
> transcribe it to Gromacs' "grammar" using a dummy shell particle to 
> describe polarizability.  Both the model with shell particle and without 
> it worked properly in the NVT ensemble. In the NVE ensemble, 
> nevertheless, the model without shell particle worked well conserving 
> energy but the model with the shell particle didn't. (with the same set 
> of parameters specially those of Ewald and Shake tolerance).
>  So is it possible that the iterative process to arrive a minimum of the 
> electric field in the shell polarization model really maps the whole 
> system from t to t+dt in a non conservative way?
>  Could I ask this question to the programmer? (did He/She implement the 
> model only for the NVT ensemble?)
>  Do someone know some paper of a NVE Ensemble employing shell 
> polarizability of any chemical nature --not only water--?

Since the minimization is of the shell position is never perfect it is 
difficult to get perfect energy conservation. By running in double 
precision and decreasing the tolerance (emtol) it can be improved to 
quite good energy conservation though.

>  I would be very thankful with the information
>  Juan S. Medina Álvarez, Ph. D.
> tlazcala at yahoo.com
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David van der Spoel, Ph.D.
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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