[Molecularmechanics] Molecular structure- Atoms and Sites

[David van der Spoel]

On Sun, 26 Oct 2003, Konrad Hinsen wrote:

>On Friday 24 October 2003 20:49, Peterson,Brian K. wrote:
>
>> 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
>
>Useful, yes, but tricky as well, because we get into the structure/force field 
>distinction again. Atoms and bonds are pretty much the same for everyone (at 
>least within what I consider to be "molecular mechanics", but interaction 
>sites are force field specific. 
>
>> 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
>
>I agree, but this does imply a force field specific desription of a system.
>
>Perhaps we should consider to define two different levels of description:
>
>1) Just the basics: atoms with basic information such as chemical element,
>    optionally bonds. That is what one would feed to visualization and
>    analysis programs. It is also what one should be able to use as a starting
>    point for building a more complete and specific model.
>
>2) A full description of the model, including interaction sites, dynamical
>   constraints, explicit force field terms (possibly referring to a predefined
>   collection of data to make the file more compact) etc.
>
>The second level would be more specific but less exchangeable. Every program 
>should be able to write out the first level as a least common denominator.
>

I've started adding a bit to the wiki at:
http://dirac.cnrs-orleans.fr/fsatom_wiki/ForcefieldData


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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