MDCompress: better, faster compression of molecular dynamics simulation trajectories.

Abstract

Molecular dynamics (MD) simulations model the physical movements of atoms in biomolecular systems over time, providing atomic-resolution insight into conformational changes, binding events, and dynamic behaviors that cannot be captured by static structures alone. As such, MD simulations are playing an increasingly important role in understanding the functional roles and molecular interactions of proteins. However, trajectories from these simulations can be extremely large, often reaching tens of gigabytes for a single simulation of modest duration. This creates substantial challenges for storage and data transfer, motivating efficient compression strategies. Furthermore, many downstream analyses require extraction of only a subset of frames or specific atoms from the full trajectory, so an ideal compression format should support rapid random-access decompression of such samplings without requiring full file decompression. Here, we introduce MDCompress, a new trajectory compression format and accompanying software implementation that meets these goals. MDCompress produces compressed trajectory files that are 15-37% smaller than those generated by the widely-used XTC format, while achieving faster compression and decompression speeds through efficient multithreading. The MDCompress software and library are released under an open license (BSD-3) and may be downloaded at https://github.com/refresh-bio/mdcompress and is also available as a Zenodo repository at 10.5281/zenodo.19218347.