Literature DB >> 24258850

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

Magnus Lundborg1, Rossen Apostolov, Daniel Spångberg, Anders Gärdenäs, David van der Spoel, Erik Lindahl.   

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.
Copyright © 2013 Wiley Periodicals, Inc.

Entities:  

Keywords:  API; compression; file format; molecular dynamics simulation

Mesh:

Substances:

Year:  2013        PMID: 24258850     DOI: 10.1002/jcc.23495

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  4 in total

Review 1.  Challenges for visualizing three-dimensional data in genomic browsers.

Authors:  Mike Goodstadt; Marc A Marti-Renom
Journal:  FEBS Lett       Date:  2017-08-24       Impact factor: 4.124

2.  libxtc: an efficient library for reading XTC-compressed MD trajectory data.

Authors:  Nikolay A Krylov; Roman G Efremov
Journal:  BMC Res Notes       Date:  2021-04-01

3.  Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case.

Authors:  Miłosz Wieczór; Vito Genna; Juan Aranda; Rosa M Badia; Josep Lluís Gelpí; Vytautas Gapsys; Bert L de Groot; Erik Lindahl; Martí Municoy; Adam Hospital; Modesto Orozco
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2022-05-30

4.  MMTF-An efficient file format for the transmission, visualization, and analysis of macromolecular structures.

Authors:  Anthony R Bradley; Alexander S Rose; Antonín Pavelka; Yana Valasatava; Jose M Duarte; Andreas Prlić; Peter W Rose
Journal:  PLoS Comput Biol       Date:  2017-06-02       Impact factor: 4.475

  4 in total

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