Hi,
there's a very recent paper of the GROMOS team, where they evaluate the
free energy of polarization (with the 'Charge-on-Spring' model):
http://pubs.acs.org/cgi-bin/abstract.cgi/jpcbfk/asap/abs/jp0706477.html
Their code is already working, but under the GROMOS software...
Ciao,
Patrick
Jones de Andrade a écrit :
Hi David
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've found two papers for charmm polariability. But I'll only be able to
try to find it in the library or to ask for the authors tomorrow at
least. But thanks for the information! ;)
On the other hand, I could not yet find any published material from
amber using shell models. Is this only an "inside group" discussion?
I think there is not a lot of difference, but shell models are easier to
implement.
I think too. In reality, there is no "visible rational reason" for this
fear of me, is more like a "feeling", so I'll try to find something more
on it.
But I do agree that it's much likely that the shell model is much easier
to implement, if not faster to execute also. :)
I am working on shell models a bit (not enough...)
Me too. Specially cause this is long terms plans (2+ years from now).
But thanks a lot for all information, David. Helped a lot.
Sincerally yours,
Jones
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Patrick FUCHS
Equipe de Bioinformatique Genomique et Moleculaire
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