title: Compressing molecular dynamics trajectories: Breaking the one-bit-per-sample barrier.
abstract: Molecular dynamics simulations yield large amounts of trajectory data. For their durable storage and accessibility an efficient compression algorithm is paramount. State of the art domain-specific algorithms combine quantization, Huffman encoding and occasionally domain knowledge. We propose the high resolution trajectory compression scheme (HRTC) that relies on piecewise linear functions to approximate quantized trajectories. By splitting the error budget between quantization and approximation, our approach beats the current state of the art by several orders of magnitude given the same error tolerance. It allows storing samples at far less than one bit per sample. It is simple and fast enough to be integrated into the inner simulation loop, store every time step, and become the primary representation of trajectory data. © 2016 Wiley Periodicals, Inc.
authors.affiliation: Biosystem Analysis Research Group, Department of Mathematics and Computer Science, Jena Centre for Bioinformatics, Friedrich Schiller University, Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany.
authors.forename: Jan
authors.initials: J
authors.lastname: Huwald
authors.affiliation: Biosystem Analysis Research Group, Department of Mathematics and Computer Science, Jena Centre for Bioinformatics, Friedrich Schiller University, Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany.
authors.forename: Stephan
authors.initials: S
authors.lastname: Richter
authors.affiliation: Biosystem Analysis Research Group, Department of Mathematics and Computer Science, Jena Centre for Bioinformatics, Friedrich Schiller University, Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany.
authors.forename: Bashar
authors.initials: B
authors.lastname: Ibrahim
authors.affiliation: Biosystem Analysis Research Group, Department of Mathematics and Computer Science, Jena Centre for Bioinformatics, Friedrich Schiller University, Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Dittrich
keywords: HRTC; TNG library; compression; molecular dynamics; trajectory