[gmx-users] Polarizability

David van der Spoel spoel at xray.bmc.uu.se
Sun May 20 20:57:22 CEST 2007

Jones de Andrade wrote:
> Hi David.
> I had no idea that gromos was using it. Also, just had a few clues that 
> maybe charmm was. All amber clues however points towards a different model.
They have published a few paper on water and alcohols. The charm crew 
have done a few more. Amber is actually split into two IIRC, with point 
dipoles as well as shell models (that means either or).

> I have a few concerns about "directioning" (really sure that this is the 
> wrong word, if exists) that a shell model polarizability would make. 
> Absolutely no doubts that it would be probably faster than any iterative 
> model include dipoles, but I have this concern.
I think there is not a lot of difference, but shell models are easier to 

> I'll be looking forward for the charmm papers on it (I've found the 
> references late this week) and try to compare its reproducibility and 
> parametrization methodologies somehow.
> About implementing it: its a good idea, but a long term one. Basically 
> it means that nobody in the developer's list seems to be working on it 
> righ now, right?  ;)
I am working on shell models a bit (not enough...)

> Thanks a lot for all answers, David.  :)
> Sincerally yours,
> Jones

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

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