[gmx-users] a future gmx 4.0 doubt

[Jones de Andrade]

Hi Prof. Spoel.

First of all, sorry for sending this message directly to your personal email
address. I was concerned that opening a thread like this would lead to
undesired discussions on the mail list, and I choosen to avoid it. Please,
forgive me for this intrusion.

I'm writing this message because I could see on the gromacs web site that
the version 4.0 is "coming to an end", if we can call it like that. I've
already asked the question I will do again, but too long time ago and now we
are in a completelly different circunstance here.

The question is about the polarization model of gromacs: is it intended to
include other models, like dipole moments interaction (like thole's one) or
fluctuating charges in gromacs 4.0, in addition to the current charge on
spring one?

Long time ago, when I made such a question, the reason was no. I'm sorry for
asking it again now, and I feel I should explain my reasons: I'm (finally)
finishing my PhD now, and will probably give a try for a pos-PhD. Maybe one
of but probably the "most exciting" possibility at moment for its project
would be an extension of the current force-fields I've been developing and
validating (soon to be published) with a polarization potential. IF
everything goes ok, we would like to give a try to other potentials, like
the ones mentioned, before choosing the best one for the types of systems we
usually work with.

That's basically the reason why I made such a question: if gromacs 4.0 is
going to release with this potentials as options, it would be fairly easy
and straight forward. If not, but there is any "movement" inside the
developers section, I would join it right now just to see how thing are
going (unfortunatelly, it would be impossible to begin to participate in
such a project right now, exactly because the finalization of the PhD). If
there is no movement for that, I would join only with 4.0 released and my
"free" time back if I get my appliance accept, in order to learn a bit more
about gromacs development and try to do this slice of the job by myself. ;)

Thanks a lot for your time, and please forgive me again for my "intrusion".
;)

Sincerally yours,

Jones

On 6/23/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> Jones de Andrade wrote:
> > Hi Mark.
> >
> > Haven't got exactly what you said. So let me rephrase myself:
> >
> > The CF4 molecule doesn't have dihedrals nor intramolecular LJ and
> > coulombic contributions.
> >
> > What kind of contribution am I missing that makes potential energy minus
> > bond stretching minus angle bending *different* from Lj + coulomb(SR) +
> > coulomb (LR) + Disp correction?
> >
> > Thanks a lot in advance,
> >
> > Sincerally yours,
> >
> > Jones
> >
> I didn't follow the whole discussion, but there are also exclusion
> corrections when using PME or RF.
>
> --
> 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
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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