[Molecularmechanics] coincidence?

[Kaihsu Tai]

Konrad Hinsen, 2004-02-05 15:28:07+0100:
> On Thursday 05 February 2004 14:52, Kaihsu Tai wrote:
> We have indeed touched some of these points in the earlier
> discussions (you can look at the archive), but the focus
> has been on the specification of a system and its
> topology. 

Are there any 'deliverables' that we can use on topology
(beyond the MMTK API)?

> Concerning trajectories, I suggest you have a look at the
> trajectory format of my Molecular Modelling Toolkit
> (http://dirac.cnrs-orleans.fr/MMTK/), which is not tied
> specifically to that software. It uses the netCDF format
> exclusively, all information required to interpret the
> data is in that one file, which I consider a significant
> practical advantage. Another advantage is that additional
> optional information can be stored in a self-documenting
> way. The format has also been optimized for different
> modes of access in analysis routines (by time step or by
> atom), and there are converters from the formats of
> CHARMM/X-Plor/NAMD, Amber, and DL-POLY, plus an inverse
> converter for CHARMM/X-Plor/NAMD.

This sounds excellent.  I have only been able to locate MMTK
API documentation on the website you cited, but not a 'raw'
description of the format.  It appears our team may want to
convert 'any' trajectory format into this MMTK format, then
use the resulting MMTK objects to write both the topology
and the trajectory into the BioSimGrid database.

> The question of "input files" (which means different
> things to different people) and coordiate/trajectory files
> has not been discussed much.

I suppose this means we are on our own with the 'input file'
issue, and will have to write our own schema.  Any advice?