[MMTK] self-contained trajectory file

Eric Pettersen pett at cgl.ucsf.edu
Tue Sep 16 00:21:52 UTC 2014

Well, obviously I'm disappointed.  On the other hand, I'm relieved I didn't miss something that was forehead-slapping obvious!

When the H5MD/Mosaic solution is further along I guess I can revisit the issue.

Thanks for the in-depth answer!


On Sep 15, 2014, at 7:03 AM, Konrad Hinsen <research at khinsen.fastmail.net> wrote:

> Eric Pettersen writes:
>> Is it possible to write a trajectory file for arbitrary chemical
>> systems that don't depend on custom database entries (i.e. all the
>> necessary information is in the trajectory file itself)?  I tried
>> using MoleculeFactory instead of subclassing Molecule, but that
>> also writes Molecules into the trajectory file to the same result.
> Short answer: There is unfortunately no way to store molecule
> definitions in trajectories, only references to the database are
> possible.
> Longer answer:
> A more flexible handling of molecule definitions has been on my to-do
> list for a long time. The MoleculeFactory class was a first step in
> this direction. Obviously I looked into storing such definitions in
> trajectories, but around the same time another limitation of the MMTK
> trajectory format became clear, which I wanted to solve at the same
> time. It's the fact that an MMTK trajectory cannot be decoded without
> MMTK (and that implies using Python), at least not with reasonable
> effort. Storing a universe as executable Python code seemed like a
> good idea in the early days of MMTK, and indeed it is a very flexible
> and at the same time simple to implement approach, but it's also too
> closely tied to MMTK. While working on a better way to store
> universes, we started discussing yet another important change to
> trajectory handling: migrating from netCDF to HDF5, mainly in order to
> profit from HDF5's support for parallel I/O, but also because of the
> added flexibility resulting from the hierarchical dataset layout.
> This is how an initially straightforward extension of the trajectory
> format turned into a major redesign that took quite a bit of time. The
> new trajectory format that MMTK will adopt is H5MD:
>   http://nongnu.org/h5md/
> H5MD was developed with the goal of suitability for a wide range of
> disciplines, which each add their own specific information. It has
> therefore no specification for describing a simulation universe. MMTK
> will use MOSAIC for this, the combination being described here:
>   http://mosaic-data-model.github.io/mosaic-specification/h5md_mosaic_module.html
> The current status of the migration is "under development". I have
> working code to convert MMTK trajectories to H5MD/MOSAIC, but nothing
> yet to produce such trajectories directly from MMTK's trajectory
> generators (MD, minimization, etc.).
> Konrad
> -- 
> ---------------------------------------------------------------------
> Konrad Hinsen
> Centre de Biophysique Moléculaire, CNRS Orléans
> Synchrotron Soleil - Division Expériences
> Saint Aubin - BP 48
> 91192 Gif sur Yvette Cedex, France
> Tel. +33-1 69 35 97 15
> E-Mail: research AT khinsen DOT fastmail DOT net
> http://dirac.cnrs-orleans.fr/~hinsen/
> ORCID: http://orcid.org/0000-0003-0330-9428
> Twitter: @khinsen
> ---------------------------------------------------------------------

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