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Re: [h5md-user] New member

From: Pierre de Buyl
Subject: Re: [h5md-user] New member
Date: Thu, 1 Sep 2011 22:04:22 +0200

Hello Konrad,

Thanks for joining us and providing your input.

As you could understand, we try to standardize first a core set of data elements and proceed then based on accumulated experience.



Le 1 sept. 11 à 19:56, Konrad Hinsen a écrit :

Hello everyone,

I just joined the group after some discussions with Pierre about HDF5 trajectories at the recent EuroSciPy conference in Paris.

A few words about my background and interest. 15 years ago, I started to write a library for biomolecular simulations in Python (with some C code for speed). It's called the Molecular Modelling Toolkit and you can get it from


At the time, I spent some time thinking about trajectory storage and I ended up choosing the netCDF format/library. HDF5 wasn't out yet, and HDF4 was much less interesting. Now we want to migrate to HDF5 for a variety of reasons, the most important ones being the parallel I/O option and the possibility to combine many datasets in a single file using HDF's hierarchical structure. So the h5md initiative comes just at the right moment.

In one aspect we are much more ambitious than h5md: we want to be able to store the full description of a molecular system, including the chemical structure of all molecules, the nature of the atoms or pseudoatoms, the rules for calculating the potential energy, and various other parameters. Since that is the hardest part, we started at that end, and by now I have a fairly useable data model for molecular systems with a Python in-memory representation and an on-disk HDF5 representation. I am currently doing extensive tests, such as converting a large subset of the Protein Data Bank (PDB) in order to see of everything in there is fully representable. I plan to make a first version public once those tests are done. What my molecular data model defines is how molecules map to atom indices in configurations and trajectories, so it should in principle fit in well with h5md, which I will of course explore.

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

Pierre de Buyl
Chemical Physics Theory Group - University of Toronto
Physique des Systèmes Complexes et Mécanique Statistique - Université Libre de Bruxelles
web: http://homepages.ulb.ac.be/~pdebuyl/

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