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An Efficient and Extensible Format, Library, and API for Binary Trajectory Data from Molecular Simulations
Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
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2014 (English)In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 35, no 3, 260-269 p.Article in journal (Refereed) Published
Abstract [en]

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. 

Place, publisher, year, edition, pages
2014. Vol. 35, no 3, 260-269 p.
Keyword [en]
molecular dynamics simulation, file format, API, compression
National Category
Natural Sciences
URN: urn:nbn:se:uu:diva-216031DOI: 10.1002/jcc.23495ISI: 000328813800008OAI: oai:DiVA.org:uu-216031DiVA: diva2:689311
Available from: 2014-01-20 Created: 2014-01-17 Last updated: 2014-01-20Bibliographically approved

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Spångberg, Danielvan der Spoel, David
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Structural ChemistryDepartment of Cell and Molecular BiologyComputational and Systems Biology
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