Jones de Andrade
johannesrs at gmail.com
Mon May 21 12:33:57 CEST 2007
Just got this paper here, thanks for the indication.
This may sound like a dumb question, but: am I wrong, or the "shell model"
and the "charge on a spring model" differ only by the fact that the VdW
interation is also "floating aroung" in the "shell model" but not in the
"charge on a spring" one?
Thanks a lot,
On 5/21/07, Patrick Fuchs <Patrick.Fuchs at ebgm.jussieu.fr> wrote:
> there's a very recent paper of the GROMOS team, where they evaluate the
> free energy of polarization (with the 'Charge-on-Spring' model):
> Their code is already working, but under the GROMOS software...
> Jones de Andrade a écrit :
> > Hi David
> > They have published a few paper on water and alcohols. The charm
> > have done a few more. Amber is actually split into two IIRC, with
> > 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
> INSERM U726, Universite Paris 7
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