Paper Citing NAMD - Abstract
Marais, Patrick; Kenwood, Julian; Smith, Keegan Carruthers; Kuttel, Michelle M.; Gain, James
Efficient compression of molecular dynamics trajectory files
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:2131-2141, OCT 15 2012
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 similar to 10-2 angstrom), we can compress a 12 fs trajectory file to 58% of its original size. For 200 fs time stepstypically used in fine grained water diffusion experimentswe can compress files to similar 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. (c) 2012 Wiley Periodicals, Inc.
