  We propose a new file format named "H5MD" for storing molecular simulation
data, such as trajectories of particle positions and velocities, along with
thermodynamic observables that are monitored during the course of the
simulation. H5MD files are HDF5 (Hierarchical Data Format) files with a
specific hierarchy and naming scheme. Thus, H5MD inherits many benefits of
HDF5, e.g., structured layout of multi-dimensional datasets, data compression,
fast and parallel I/O, and portability across many programming languages and
hardware platforms. H5MD files are self-contained and foster the
reproducibility of scientific data and the interchange of data between
researchers using different simulation programs and analysis software. In
addition, the H5MD specification can serve for other kinds of data (e.g.
experimental data) and is extensible to supplemental data, or may be part of an
enclosing file structure.
