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
implement.
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.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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