H5MD : HDF5 for molecular data

H5MD is a file format specification, based upon HDF5, aimed at the efficient and portable storage of molecular data (e.g. simulation trajectories, molecular structures, …). H5MD implements data models for a variety of computational problems, e.g., molecular simulation using molecular dynamics, or computational fluid dynamics using multi-particle collision dynamics.

The first release of the specification, H5MD 1.0.0, describes the storage of particle trajectories (positions, velocities, forces and species) as well as thermodynamical observables. Future extensions will be considered on the basis of discussion with users of H5MD.

The development of H5MD was started by Pierre de Buyl, Peter Colberg and Felix Höfling. H5MD now includes contributions by other developers. H5MD is available under the GNU General Public License version 3, or any later version. H5MD is presented in P. de Buyl, P. H. Colberg and F. Höfling, H5MD: A structured, efficient, and portable file format for molecular data, Comp. Phys. Comm. 185, 1546–1553 (2014) [arXiv:1308.6382].

Getting the specification

The H5MD format specification is maintained in a git repository:

git clone http://git.savannah.gnu.org/r/h5md.git

The latest revision is also available in PDF.


If you want to know more about or contribute to H5MD, please visit the project page of H5MD or join the mailing list. An archive of previous posts can be searched in the mailing list archive.