ZarrMD specification

The zarrmd trajectory file format uses the H5MD file format as a directory structure and metadata specification for storing molecular dynamics simulation data in the Zarr file format.

zarrmd files are exactly the same as H5MD files, but with the .zarrmd extension, except for one broken H5MD layout requirement: H5MD requires that the ‘step’ and ‘time’ datasets of the ‘particles’ trajectory group’s simulation box must be hard linked to the ‘step’ and ‘time’ datasets of the corresponding trajectory groups’ ‘positions’ dataset.

This is not possible in Zarr, so this requirement is relaxed in zarrmd such that the ‘step’ and ‘time’ datasets of the ‘particles’ trajectory group in the simulation box and positions datasets are required to contain the exact same shape and data, but are not required to be hard linked.

For more information, see the H5MD Specification