Free/Libre software for H5MD files

This is a list of free software for use with H5MD files.

Reading and writing H5MD files

The HDF5 library provides interfaces for C, Fortran, C++, and Java.

HDF5 for Python provides a Pythonic interface to the HDF5 binary data format.

h5xx is a thin C++ wrapper to ease reading and writing of HDF5 files.

fortran_h5md is a Fortran module to facilitate the writing of H5MD files.

pyh5md is a Python module that facilitate reading and writing H5MD files.

ch5md is a set of C routines to read and write H5MD files.


HAL’s MD package is a high-precision molecular dynamics package for the large-scale simulation of simple and complex liquids.

ESPResSo is a highly versatile software package for scientific molecular dynamics simulations of coarse-grained atomistic or bead-spring models for soft matter research.

ESPResSo++ is a software package for the scientific simulation and analysis of coarse-grained atomistic or bead-spring models as they are used in soft matter research.

LAMMPS is a classical molecular dynamics code with a focus on materials modeling. It’s an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. See command dump h5md.

Analysis and plotting

h5md-tools is a tool set for analysing, plotting, and manipulating data of molecular simulations stored in the H5MD file format.

MDAnalysis is a Python library for analysing trajectories from molecular simulations, including the H5MD file format. Version 2.0.0 features parallel I/O using MPI, see Jakupovic & Beckstein, 2021.

VMD-h5mdplugin is a H5MD file reader plugin for the molecular visualization program VMD.

VOTCA is an analysis package for molecular dynamics data that focuses on systematic coarse-graining and microscopic charge transport.