[h5md-user] H5MD for proteins

[Konrad Hinsen]

Hi everyone,

I have been rather quiet on this list for a while, mostly because I
was busy with other things, but I still read the messages to follow
progress, which looks very encouraging.

As I mentioned earlier (long ago by now), for the question of
trajectory storage is inseparable from the question of storing a
definition of the system that is being simulated. There is no point
(for me at least) in having a trajectory from which I can pick the
coordinates of atom 532 without having the slightest idea of what atom
532 represents in my system.

I have been working on that aspect, which is not limited to
trajectories, and came up with a data model for molecular simulations:

  http://bitbucket.org/molsim/mosaic/wiki/Home

Its HDF5 implementation should be compatible with H5MD, though I will
be sure only once I try to use both together. That's my project for
the near future.

A Mosaic universe defines molecular structures, a topology for the
entire system (i.e. periodic boundary conditions and symmetry
transforms), and how many copies of each molecule are present in the
system. It provides an atom order that can serve as the link to the
data in H5MD files. In HDF5, a universe is stored in a group, which
could sit nicely next to the h5md group.

I'll post a few more specific questions about the current H5MD
definition in separate threads, this message is just to provide
the context for them.

Konrad
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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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