Gromacs

File formats

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    A replacement for the gromacs file formats xtc/trr/edr is needed for the following reasons:

    1. Ease of use of a single file compared to handling three files
    2. Support for parallel I/O for large parallel calculations

    The following demands / specification should be adhered to

    1. Portable accross UNIX (including Linux and Mac OSX) and Windows platforms
    2. Support for large files (2Gb on all platforms)
    3. Support for frames that are more than 2Gb
    4. 64 bit integers for all integer variables
    5. Flexible I/O - possibility to store different variables, e.g. lambda's per atom
    6. Support for varying number of particles (for Grand Canonical MD) in a manner such that stupid program won't crash
    7. Built-in indexing for fast searching
    8. Transparent use in analysis applications
    9. Compatibility with checkpointing
    10. Arbitrary extra data per frame (e.g. history)
    11. Dealing with low memory on the master node (for very large simulations)

    In early 2011 the "Trajectory Next Generation" paper was  published (http://dx.doi.org/10.1007/s00894-010-0948-5). The TNG format covers most of the demands and it is available from http://www.uppmax.uu.se/Members/daniels/trajng-trajectory-compression-library.

    An implementation of the file format in GROMACS will be provided in a git branch.

    The attached README file below covers most of what you need to know to use the library.

    Page last modified 07:44, 3 Apr 2011 by spoel