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An efficient and extensible format, library, and API for binary trajectory data from molecular simulations

Authors

  • Magnus Lundborg,

    1. Department of Theoretical Physics and Swedish e-Science Research Center, Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
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  • Rossen Apostolov,

    1. PDC Center for High Performance Computing, Royal Institute of Technology, Teknikringen 14, SE-100 44 Stockholm, Sweden and Science for Life Laboratory, Solna, Sweden
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  • Daniel Spångberg,

    1. Department of Chemistry—Ångström Laboratory, Uppsala Multidisciplinary Center for Advanced Computational Methods (UPPMAX), Uppsala University, Uppsala, Sweden
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  • Anders Gärdenäs,

    1. Department of Cell and Molecular Biology, Uppsala Center for Computational Chemistry, Uppsala University, Uppsala, Sweden
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  • David van der Spoel,

    1. Department of Cell and Molecular Biology, Uppsala Center for Computational Chemistry, Uppsala University, Uppsala, Sweden
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  • Erik Lindahl

    Corresponding author
    1. Department of Theoretical Physics and Swedish e-Science Research Center, Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
    2. Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, Stockholm, Sweden
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Abstract

Molecular dynamics simulations is an important application in theoretical chemistry, and with the large high-performance computing resources available today the programs also generate huge amounts of output data. In particular in life sciences, with complex biomolecules such as proteins, simulation projects regularly deal with several terabytes of data. Apart from the need for more cost-efficient storage, it is increasingly important to be able to archive data, secure the integrity against disk or file transfer errors, to provide rapid access, and facilitate exchange of data through open interfaces. There is already a whole range of different formats used, but few if any of them (including our previous ones) fulfill all these goals. To address these shortcomings, we present “Trajectory Next Generation” (TNG)—a flexible but highly optimized and efficient file format designed with interoperability in mind. TNG both provides state-of-the-art multiframe compression as well as a container framework that will make it possible to extend it with new compression algorithms without modifications in programs using it. TNG will be the new file format in the next major release of the GROMACS package, but it has been implemented as a separate library and API with liberal licensing to enable wide adoption both in academic and commercial codes. © 2013 Wiley Periodicals, Inc.

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