MDAnalysis

The goal of MDAnalysis is to make it easy for users to analyze data that are produced by simulations (primarily molecular dynamics simulations) that run on some of the largest supercomputers in the world. MDAnalysis accomplishes this goal by providing a toolkit of programming building blocks that provide an abstract Python interface to the simulation data — agnostic of the specific simulation package that produced it — that lends itself to interactive data exploration and rapid prototyping but is also a robust foundational library that can form the basis for new computational tools.

MDAnalysis allows one to read particle-based trajectories such as the ones produced by MD simulations or individual coordinate frames (such as biomolecules in the Protein Databank format) and access the atomic coordinates through NumPy arrays. Together with a powerful selection language and many implemented analysis algorithms, MDAnalysis provides a flexible and fast framework for complex analysis tasks. Welcoming documentation such as the User Guide https://userguide.mdanalysis.org/ make it easy to get started. New releases are downloaded a few thousand times and the academic papers describing MDAnalysis are cited more than almost two thousand times, indicating the widespread use in the academic community.