[Top][All Lists]

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

[h5md-user] New member

From: Konrad Hinsen
Subject: [h5md-user] New member
Date: Thu, 1 Sep 2011 19:56:19 +0200

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

reply via email to

[Prev in Thread] Current Thread [Next in Thread]