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[h5md-user] Subgroups

From: Konrad Hinsen
Subject: [h5md-user] Subgroups
Date: Mon, 9 Sep 2013 12:43:32 +0200

One of the points that are unclear to me in the current specification
is the definition of subgroups.

Suppose I have a system consisting of a protein in solvent. I want to
have two subgroups, "protein" and "solvent". But I also have data that
applies to the whole system, without breaking it down into subgroups.
And I might have yet another data set that uses different subgroups
for a specific purpose.

My understanding of the current specification is that particles
are numbered from 0 to N-1 inside each subgroup. I would have
atoms number 0 to K-1 for my protein, and 0 to L-1 for my solvent.
Then how do I know what these atoms correspond to in the complete
system? That information cannot be deduced from the data for each
subgroup, so it has to be supplied somewhere else. But where?

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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