Efficient Compression of Molecular Dynamics Trajectory Files

Marais, Patrick and Kenwood, Julian and Carruthers Smith, Keegan and Kuttel, Michelle M and Gain, James (2012) Efficient Compression of Molecular Dynamics Trajectory Files, Journal of Computational Chemistry, 33, 2131-2141, Wiley Subscription Services, Inc..

Full text not available from this repository. (Use alternate locations listed below)


We investigate whether specific properties of molecular dynamics trajectory files can be exploited to achieve effective file compression. We explore two classes of lossy, quantized compression scheme: "interframe" predictors, which exploit temporal coherence between successive frames in a simulation, and more complex "intraframe" schemes, which compress each frame independently. Our interframe predictors are fast, memory-efficient and well suited to on-the-fly compression of massive simulation data sets, and significantly outperform the benchmark BZip2 application. Our schemes are configurable: atomic positional accuracy can be sacrificed to achieve greater compression. For high fidelity compression, our linear interframe predictor gives the best results at very little computational cost: at moderate levels of approximation (12-bit quantization, maximum error ~ 10−2 Å), we can compress a 1–2 fs trajectory file to 5–8% of its original size. For 200 fs time steps—typically used in fine grained water diffusion experiments—we can compress files to ~25% of their input size, still substantially better than BZip2. While compression performance degrades with high levels of quantization, the simulation error is typically much greater than the associated approximation error in such cases

Item Type: Journal article (paginated)
Additional Information: http://dx.doi.org/10.1002/jcc.23050
Uncontrolled Keywords: MD trajectory files compression arithmetic coding interframe prediction
Subjects: Applied computing > Life and medical sciences
Computing methodologies
Mathematics of computing > Information theory
Date Deposited: 22 Oct 2012
Last Modified: 10 Oct 2019 15:33
URI: http://pubs.cs.uct.ac.za/id/eprint/803

Actions (login required)

View Item View Item