[Molecularmechanics] Re: Some general remarks.

[David]

On Wed, 2003-11-19 at 05:48, Martin Field wrote:
> Hi all,
>  
>    I've been reading the posting on the list
> with interest and have a couple of remarks.
>  
>    Currently, it seems that the emphasis of
> the discussion is upon how to specify the
> composition of the system in terms of fragments
> or molecules. This is because dealing with
> force-fields has been deemed too complicated
> (at least for the moment).
>  
>    Clearly both problems are important, but
> it would seem to me that tackling the force-field
> problem is in some ways easier than the composition
> problem and that the latter could have a more immediate
> impact in the MM area.
>  
>    Some points (and questions):
>  
> 1. Specifying composition is not a problem unique
>    to MM simulations. Conventions to do so already exist
>    and no doubt there are ongoing efforts as well.
>    How much overlap is there with these?
>  
> 2. Is a unique convention desirable? Thus, for example,
>    a PDB or a CIF-like convention may be most appropriate
>    for biomolecule people but other conventions may be
>    more suitable in other areas.
>  
> 3. Most simulation programs that I am familiar
>    with generate explicit lists of atoms, force-field
>    terms, force-field parameters, etc. when they
>    generate a force-field for a particular system.
>    Most of these can also write and reread this
>    information so that the force-field generation
>    step does not have to be repeated.
>  
>    I think it would be a useful first step and
>    relatively straightforward to come up with a
>    (XML) representation of this data. To be more
>    concrete, a file or files that do the same thing
>    as AMBER top files or CHARMM psf and parameter
>    files. 
>  
> Any comments?

On the WIKI you'll find a short description of what I think is important
to cover. Please go  check the list and make additions to it. (do add
your name and maybe a data as well).

http://dirac.cnrs-orleans.fr/fsatom_wiki/ForcefieldData
>  
> Cheers,
>  
> Martin Field.
-- 
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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