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Trajectory NG: portable, compressed, general molecular dynamics trajectories
Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
2011 (English)In: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 17, no 10, 2669-2685 p.Article in journal (Refereed) Published
Abstract [en]

We present general algorithms for the compression of molecular dynamics trajectories. The standard ways to store MD trajectories as text or as raw binary floating point numbers result in very large files when efficient simulation programs are used on supercomputers. Our algorithms are based on the observation that differences in atomic coordinates/velocities, in either time or space, are generally smaller than the absolute values of the coordinates/velocities. Also, it is often possible to store values at a lower precision. We apply several compression schemes to compress the resulting differences further. The most efficient algorithms developed here use a block sorting algorithm in combination with Huffman coding. Depending on the frequency of storage of frames in the trajectory, either space, time, or combinations of space and time differences are usually the most efficient. We compare the efficiency of our algorithms with each other and with other algorithms present in the literature for various systems: liquid argon, water, a virus capsid solvated in 15 mM aqueous NaCl, and solid magnesium oxide. We perform tests to determine how much precision is necessary to obtain accurate structural and dynamic properties, as well as benchmark a parallelized implementation of the algorithms. We obtain compression ratios (compared to single precision floating point) of 1:3.3-1:35 depending on the frequency of storage of frames and the system studied.

Place, publisher, year, edition, pages
Berlin/Heidelberg: Springer , 2011. Vol. 17, no 10, 2669-2685 p.
Keyword [en]
Molecular dynamics, Trajectory, Compression
National Category
Natural Sciences Inorganic Chemistry
Research subject
Chemistry with specialization in Inorganic Chemistry
Identifiers
URN: urn:nbn:se:uu:diva-149412DOI: 10.1007/s00894-010-0948-5ISI: 000295940700024PubMedID: 21267752OAI: oai:DiVA.org:uu-149412DiVA: diva2:404944
Available from: 2011-03-19 Created: 2011-03-19 Last updated: 2017-12-11Bibliographically approved

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Spångberg, DanielLarsson, Danielvan der Spoel, David

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