[Molecularmechanics] Next version of invite

[Michael Shirts]

Thanks for all your responses and suggestions!  I can tell that
we're going to be able to do a lot.

Two suggestions as unofficial organizer-until-the-group-is-together:

1. I think we should hold off getting to work too seriously until we've got a
few more of the major players involved.  We don't want then to feel on the
outside looking in.  This should only be a week or so - if they haven't signed
on by then, it's their own fault.

2. Based on the conversation, I think we really should focus first on
structural formats (both input and ouput -- this includes trajectories), and
not work on force field representations initially. Once we have a sense for
the dynamics of the group, and have something we all agree on, we can move on
to harder topics.

3. Thanks for the comments on the letter.  Here's the latest draft.  If I
don't get any comments, this will be sent out in 24 hours.  I have added
developers to the list, and I have changed all references to the workgroup as
"workgroup on molecular mechanics", instead of "biomolecular simulation, while
making it clear that we are especially interested in representations of
biological molecules.

NWCHEM : ?? (It's very unclear from the web page who's in charge of
	the molecular mechanics aspects -- please let me know if
	you know the contact info.
Schrodinger (Macromodel, Impact): Tom Halgren <halgren@schrodinger.com>
GROMOS : Wilfred van Gunsteren <biomos@igc.phys.chem.ethz.ch>
DL-POLY : Bill Smith <w.smith@dl.ac.uk>
DL-PROTEIN : Simone Melchionna <@roma1.infn.it>
BOSS/MCPRO : Bill Jorgensen <William.Jorgensen@yale.edu>,
             Julian-Tirado Rivas <Julian.Tirado-Rives@yale.du>
MOIL: Ron Elber <ron@fh.huji.ac.il>

It was also mentioned that we involve the molecular graphics guys from
the beginning, as they will have some valuable input.

PyMOL : Warren DeLano <warren@delanoscientific.com>
VMD : Jim Phillips <jim@ks.uiuc.edu>
gOpenMol: Leif Laaksonen <gopenmol@csc.fi>, <Leif.Laaksonen@csc.fi>
WhatIF : Gert Vriend <Vriend@CMBI.KUN.NL>
molden : Gijs Schaftenaar <G.Schaftenaar@cmbi.kun.nl>

If there are any other major visualization codes, please let me know,
including contact info. (RasMol seens to have fragmented, so I didn't include
it).

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 molecular mechanics.  Currently the molecular
mechanics developers that have agreed to work together for open standards
represent CHARMM, AMBER, NAMD, GROMACS, MMTK, 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 molecular mechanics is
developing a standard file format for structural information -- both for input
structures, and for output trajectories.  We are most interested in
biomolecular simulations, but we aim to make the standards general enough to
include all atomistic structural information at resolution coarser than that
of electronic structure - i.e., polarization and other atomic descriptors will
probably be supported, electronic structure will probably not.

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/MolecularMechanicsOpenStandards 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 developers 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.
You can also sign up directly at:
http://www.tddft.org/mailman/listinfo/molecularmechanics

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


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