Re: [h5md-user] New member

[Pierre de Buyl]

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.

Regards,

Pierre

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
>
>         http://dirac.cnrs-orleans.fr/MMTK/
>
> 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.
> --
> ---------------------------------------------------------------------
> 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
> ---------------------------------------------------------------------



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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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