[Molecularmechanics] first steps

[Konrad Hinsen]

On Tuesday 21 October 2003 02:57, Michael Shirts wrote:
> Hi, all-
>
> I've posted a first draft of the plan at:
>
> http://dirac.cnrs-orleans.fr/fsatom_wiki

Thanks! I added links for all the software packages - links are always good.

I noticed that you used the term "Working Group on Biomolecular Simulation" 
instead of "Molecular Mechanics". I think we should agree as early as 
possible on what application domain is that we wish to cover. I see it as 
molecular mechanics in the widest sense, including biomolecules but not 
limited to it. Indeed, one of my major complaints about the PDB file format 
is that it is very unsuited for non-biomolecular systems. While biomolecules 
are certainly the most difficult aspect of our work, we shouldn't lose track 
of the rest and end up with a file format where liquid argon has to be 
described as an unconnected sequence of one-atom residues.

> Also, below is a draft of the letter I plan to send out.  Please let me
> know if you have any comments.  The people/code groups that we would like
> to get involved are listed below.  Please tell me if you know the correct
> contact people, or if there are other code bases that should be added.
>
> NAMD : Klaus Schulten, Robert Skeel, Emad Tajkhorshid, ??
> NWCHEM : ??
> Schrodinger (Macromodel, Impact): Tom Halgren
> GROMOS : van Gunsteren
> D-POLY : ??

The person to contact for DL-POLY is Bill Smith <w.smith@dl.ac.uk>. There is 
also DL_PROTEIN, a derivate with some protein support, which comes from 
Italy, the person to contact is Simone Melchionna.

Konrad.
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