MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories
RT McGibbon and KA Beauchamp and MP Harrigan and C Klein and JM Swails and CX Hernandez and CR Schwantes and LP Wang and TJ Lane and VS Pande, BIOPHYSICAL JOURNAL, 109, 1528-1532 (2015).
As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user- friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python.
Return to Publications page