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An efficient and extensible format, library, and API for binary trajectory data from molecular simulations.
Lundborg, Magnus; Apostolov, Rossen; Spångberg, Daniel; Gärdenäs, Anders; van der Spoel, David; Lindahl, Erik.
Afiliação
  • Lundborg M; Department of Theoretical Physics and Swedish e-Science Research Center, Royal Institute of Technology, Science for Life Laboratory, Box 1031, SE-171 21, Solna, Sweden.
J Comput Chem ; 35(3): 260-9, 2014 Jan 30.
Article em En | MEDLINE | ID: mdl-24258850
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.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Software / Processamento Eletrônico de Dados / Simulação de Dinâmica Molecular Limite: Animals Idioma: En Revista: J Comput Chem Assunto da revista: QUIMICA Ano de publicação: 2014 Tipo de documento: Article País de afiliação: Suécia

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Software / Processamento Eletrônico de Dados / Simulação de Dinâmica Molecular Limite: Animals Idioma: En Revista: J Comput Chem Assunto da revista: QUIMICA Ano de publicação: 2014 Tipo de documento: Article País de afiliação: Suécia