[gmx-users] Polarizability

Jones de Andrade johannesrs at gmail.com
Sun May 20 19:49:09 CEST 2007

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.

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'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?  ;)

Thanks a lot for all answers, David.  :)

Sincerally yours,


On 5/20/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> Jones de Andrade wrote:
> > Hi list.
> >
> > Well, a few days ago I've written a message concerning the future
> > implementations that could be expected min gromacs 4 when it's released.
> > Unfortunatelly, the thread hasn't gone any further.
> lots of plans, but no promises. we really don't want to raise any
> expectations, more than significantly increased performance both
> sequential and parallel.
> >
> > So, I would like to know if there is somone in this list who ever tried
> > to modify gromacs program forces and energies routines. More
> > specifically, if someone has tried to somehow implement any
> > polarizability model in the force field, other than the "shells" model.
> >
> no plans. the shell model will most likely be the dominant model, both
> gromos and charmm developers are using it now.
> if you feel like implementing other stuff yourself, you're welcome to
> continue the discussion on the developer list.
> --
> 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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