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MDAnalysis
API docs (stable)
API docs (development)
MDAKits

Getting started

Installation
Quick start guide
Frequently asked questions
Examples
MDAnalysis Release Notes

Data structures

Universe
AtomGroup
Groups of atoms
Atom selection language
The topology system

Trajectories

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

Input/output

Reading and writing files
Format overview
Guessing
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

Format reference
INPCRD, RESTRT (AMBER restart files)
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INPCRD, RESTRT (AMBER restart files)

MDAnalysis can read coordinates in Amber coordinate/restart files (suffix “inpcrd”).

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© Copyright 2019-2023, Lily Wang, Irfan Alibay, Patricio Barletta, Cédric Bouysset, Jan Domanski, Bjarne Feddersen, Florent Langenfeld, Hugo MacDermott-Opeskin, Micaela Matta, Rocco Meli, Paul Smith, Mieczyslaw Torchala, Mark Verma, Yuxuan Zhuang, Richard J. Gowers, and Oliver Beckstein.. Revision 698e0839.

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