Compressing molecular dynamics trajectories: breaking the one-bit-per-sample barrier

TL;DR

The paper introduces HRTC, a novel compression scheme for molecular dynamics trajectories that significantly reduces storage requirements by approximating quantized data with piecewise linear functions, surpassing existing methods.

Contribution

HRTC is a new high-resolution compression algorithm that achieves sub-one-bit-per-sample storage, outperforming current state-of-the-art domain-specific compression techniques.

Findings

HRTC beats current methods by several orders of magnitude at the same error tolerance.

It enables storing trajectory data at far less than one bit per sample.

The approach is simple, fast, and suitable for integration into simulation loops.

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.