File Formats

In MDANSE 2, there have been significant changes to the supported file formats for input and output. This section provides an overview of these changes and the file formats used by MDANSE.

HDF5 Based File Formats

In MDANSE 2, the primary file format for both trajectory (MDT) storage and analysis (MDA) results are based on the Hierarchical Data Format (HDF5) . HDF5 is a versatile file format designed for efficiently organizing and managing large data sets. It employs a hierarchical structure, akin to a file system, and supports n-dimensional arrays with associated metadata attributes. HDF5 is widely adopted, and even NetCDF version 4 is built on top of HDF5. Using HDF5 ensures platform independence, efficient data storage, and self-contained information within trajectory files.

Trajectories have to be converted to the MDT format before they can be analysed with MDANSE. Multiple converters are available in MDANSE to convert outputs of different MD engines to the MDT format.

The results of MDANSE analysis runs are saved in MDA files. Contents of the MDA files can be viewed and plotted in the MDANSE GUI.

DAT File Format

An alternative output format of analysis results is in the form of DAT files, which are text-based and easily readable. Each DAT file corresponds to a specific variable generated during the analysis. If the TextFormat option is selected, a tarball is generated, which contains multiple files, including:

  • jobinfo.txt: A text file documenting the analysis options selected during the analysis.

  • DAT Files: Each file is named after the variable it contains and includes the following information:

    • Variable name

    • Type of plot (representing plot dimensions)

    • Variable’s placement on the x-axis (if plotted on the y-axis in the 2D/3D Plotter)

    • Units of data

    • Length of the trajectory (indicated as slice:[length])

    • A list of numbers representing the variable data

The DAT format simplifies data sharing and analysis, providing a clear and human-readable representation of analysis results.

CSV files

Instead of writing the results straight into a text file, it is also possible to export the results to a CSV file in post-processing, using the data plotter. More details on this can be found in Data as Text.

H5MD Files

When created according to the standard, H5MD trajectories contain all the information needed by MDANSE to load, visualise and analyse them. You should be able to load an H5MD trajectory into MDANSE GUI without converting it to the MDT format.

Some popular MD engines provide packages for writing H5MD files, but the resulting files do not include essential information such as the physical units of time, positions and velocities. Please try out your MD engine’s H5MD implementation using a very short MD run. If you are not able to load the resulting H5MD file into MDANSE, please use the engine’s standard trajectory format for other runs.