Logo
2.10.0-dev0
  • MDAnalysis
  • API docs (stable)
  • API docs (development)
  • MDAKits

Getting started

  • Installation Guide
  • Quick start guide
  • Frequently asked questions
  • Examples
  • MDAnalysis Release Notes

Data structures

  • Universe
  • AtomGroup
  • Groups of atoms
  • Atom selection language
  • The topology system
  • Guessing Topology Attributes

Trajectories

  • Trajectories
  • Slicing trajectories
  • On-the-fly transformations
  • Units and constants

Input/output

  • Reading and writing files
  • Format overview
  • Auxiliary files
  • Selection exporters
  • Format reference

Analysis

  • Analysis
  • Alignments and RMS fitting
  • Distances and contacts
  • Trajectory similarity
  • Structure
  • Volumetric analyses
  • Dimension reduction
  • Polymers and membranes
  • Hydrogen Bond Analysis
  • Writing your own trajectory analysis
  • Parallelizing analysis

Advanced

  • Standard residues in MDAnalysis selections
  • Advanced topology concepts
  • Example data

Contributing

  • Contributing to MDAnalysis
  • Contributing to the main codebase
  • Contributing to the user guide
  • Preparing a release
  • Module imports in MDAnalysis
  • Tests in MDAnalysis
  • References
MDAnalysis User Guide
  • Search

© Copyright 2019-2025, Lily Wang, Irfan Alibay, Patricio Barletta, Cédric Bouysset, Rubén Chaves, Jan Domanski, Bjarne Feddersen, Mike Henry, Florent Langenfeld, Hugo MacDermott-Opeskin, Micaela Matta, Rocco Meli, Mahfuza Humayra Mohona, Paul Smith, Mieczyslaw Torchala, Mark Verma, Yu-Yuan (Stuart) Yang, Yuxuan Zhuang, Richard J. Gowers, and Oliver Beckstein..

Please see our Privacy Policy to learn how MDAnalysis collects data.