[Molecularmechanics] Molecular structure- Atoms and Sites

[David]

On Fri, 2003-10-24 at 23:25, David wrote:
> On Fri, 2003-10-24 at 20:49, Peterson,Brian K. wrote:
> > I have a comment that mixes somewhat the discussions on force-field representation and structure representation.  Looking forward to new kinds of force-fields etc., might it be useful to describe structures as collections of sites and bonds rather than atoms and bonds?  Of course one can think of dummy-atom = site, but it seems conceptually more clear to me and potentially more flexible to have an atom being composed of at least one site and a molecule as a collection of atoms, sites, and bonds.  The most obvious use for such a distinction is to have sites which hold charge and which can be placed at essentially arbitrary locations.  An oxygen atom could consist of a nuclear site and sites for lone pairs etc.  These non-atom sites could also be useful since they will not have names in the periodic table and could easily be suppressed or not as desired in a gui.  They could also function as markers within a structure than might have nothing to do with the physics or chemi!
 st!
>  ry!
> > , but would live within our structure representation.  Of course this adds complexity, but the flexibility might be worth it ????
> > 
> Very good point, not only is there TIP4P/TIP5P, plus numerous
> polarizable models that have virtual sites, proteins can also contain
> them (for reasons of efficiency). It would be very nice indeed if
> graphics programs could be told to ignore these sites.
> 

To add on to this, I can say that in gromacs we distinguish three
particle types:

atom (obvious)
dummy (virtual site)
shell (for electronic degrees of freedom)



-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. 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@xray.bmc.uu.se	spoel@gromacs.org   http://xray.bmc.uu.se/~spoel
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