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Re: [h5md-user] H5MD for proteins

From: Konrad Hinsen
Subject: Re: [h5md-user] H5MD for proteins
Date: Tue, 10 Sep 2013 08:12:26 +0200

Pierre de Buyl writes:

 > H5MD attempts to be rather generic. The module/convention in the other thread
 > could be a satisfactory solution.

Indeed. But one question one needs to ask is: what's the goal of
"bare" H5MD?  What can one do with a trajectory file if all one knows
is that it's a valid H5MD file?

For now I see mainly visualization of trajectory contents, plus some
very specific calculations. For example, one could compute the center
of mass of a subgroup. Computing the center of mass of two subgroups
is already impossible without additional assumptions, because the
positions of two different subgroups could be stored in different
units that are unknown.

 > Do you mean that Mosaic-HDF5 would sit on top of H5MD?

Not in general, just for trajectories. A trajectory would be
an H5MD file with a Mosaic universe (another HDF5 group) sitting
next to the h5md directory. With a definite name for that universe,
we'd have our first module.

 > > 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.
 > Welcome back then :-)

Thanks! And thanks for all the work you all did on H5MD. I know
it's a lot of work which most outsiders don't appreciate as much
as they should.

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
ORCID: http://orcid.org/0000-0003-0330-9428
Twitter: @khinsen

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