Rationale

This plugin enables VMD to display dynamic molecular data stored in H5MD files.

H5MD is a structured, binary file format for molecular data, such as simulation trajectories, molecular structures, or particle subsets with associated data. In addition, there is scope for custom data.

H5MD is built on the HDF5 library and provides, among others, multi-dimensional datasets, data compression, high-performance parallel I/O, and portability.

H5MD files are created by these simulation packages:

• HAL’s MD package
• ESPResSo
• LAMMPS (h5md dump style)

Find out about more H5MD-related software.

The H5MD file specification is hosted at http://nongnu.org/h5md and has been published originally in P. de Buyl, P. H. Colberg, and F. Höfling, Comput. Phys. Commun. 185, 1546 (2014), see also arXiv:1308.6382.

Installation

To compile the plugin, run make. This should work on any Unix that has VMD and HDF5 installed. Under Ubuntu, the latter is provided by the package libhdf5-dev.

Alternatively, you may build the plugin via CMake (cmake && make).

To load the plugin in VMD add the following line to your ~/.vmdrc (replace the directory to where you have compiled it):

    vmd_plugin_scandirectory /PATH_TO_SO_DIRECTORY/ h5mdplugin.so

Alternatively you may also load the plugin by linking h5mdplugin.so and libh5md.so into the vmd molfile plugins folder (e.g. under .../vmd/plugins/LINUXAMD64/molfile/). You can do this automatically via make install.

Remarks

• The plugin only works with three-dimensional position data.

• The files libh5md.c and libh5md.h form a small library which provides common C routines to read and write H5MD files. This library is licensed under GPLv3.

• In order to make full usage of VMD (for example to make VMDs output more "colourful") you need to specify the dataset /parameters/vmd_structure in your h5md file, the documentation for this dataset can be found in the file "Documentation VMD parameters".

Examples

Example h5md files can be found in the folder "samples".