[Molecularmechanics] first steps

[Michael Shirts]

Hi, all-

I've posted a first draft of the plan at:

http://dirac.cnrs-orleans.fr/fsatom_wiki

Please take a look and let me know if any changes need to be made.

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 plan is to send this letter out, and wait for the first round, and
then send a second round to the people who didn't respond the first
time, with all the additional people who signed on from tyhe first
round.  Hopefully, they will see at that point that they are
outnumbered, and had better sign on if they know what's good for them :)

Cheers,
Michael

***************************************

Dear ,

At a recent meeting CECAM meeting, sponsored by the FSatom project
(http://www.fsatom.org) a working group was formed to try
to develop open standards in the field of biomolecular computing.
Currently the molecular mechanics developers that have agreed to work
together for open standards represent CHARMM, AMBER, GROMACS, and
TINKER.  We hope that as many code base developers as possible will be
able to join the effort.

The initial plan for the FSatom "Working group for biomolecular
simulation" is developing a standard file format for structural
information -- both for input structures, and for output trajectories.
Other projects in developing standards for other input parameters and
for force fields are being considered, but as there is significantly
more variation among the diversity of code bases in these file formats
and inputs, any work on these will wait until after the development of
formats for the relatively straightfoward structural file
formats. Please visit http://dirac.cnrs-orleans.fr/fsatom_wiki for a
further description of the current plan for the working group.

The comittment time is expected to be small.  The majority of the work
will be conducted online, with conference calls as deemed necessary
and very occasionally meetings in person if they are deemed necessary
by the participants.  No committment to support the final version of
the open standard by the participant is required, though it will, of
course, be strongly encouraged.

Please reply to mrshirts@stanford.edu to receive further information
and to be put on the mailing list, or if you have additional questions
about the FSatom project or the biomolecular working group.

Michael Shirts
Pande Research Group
Department of Chemistry
Stanford University
http://www.folding.org