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,
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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