[Molecularmechanics] Next version of invite

[Pengyu Ren]

Hi Michael,

	  Very minor suggestion: write down the list of packages in alphabetic order (amber, charmm....) -:)

Regards,
Pengyu


======= 2003-10-24 10:22:00 original messages===

>
>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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