MDAnalysis documentation

Release:2.1.0-dev0
Date:Sep 06, 2021

MDAnalysis (www.mdanalysis.org) is an object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, Amber, NAMD, LAMMPS, DL_POLY and other packages; it also reads other formats (e.g., PDB files and XYZ format trajectories; see Table of supported coordinate formats and Table of Supported Topology Formats for the full lists). It can write most of these formats, too, together with atom selections for use in Gromacs, CHARMM, VMD and PyMol (see Selection exporters).

It allows one to read molecular dynamics trajectories and access the atomic coordinates through NumPy arrays. This provides a flexible and relatively fast framework for complex analysis tasks. Fairly complete atom Selection commands are implemented. Trajectories can also be manipulated (for instance, fit to a reference structure) and written out in a range of formats.

Getting involved

Please report bugs or enhancement requests through the Issue Tracker. Questions can also be asked on the mdnalysis-discussion mailing list.

The MDAnalysis community subscribes to a Code of Conduct that all community members agree and adhere to — please read it.

User Guide

The MDAnalysis User Guide provides comprehensive information on how to use the library. We would recommend that new users have a look at the Quick Start Guide. The User Guide also has a set of examples on how to use the MDAnalysis library which may be of interest.

Installing MDAnalysis

The easiest approach to install the latest release is to use a package that can be installed either with conda or pip.

conda

First installation with conda:

conda config --add channels conda-forge
conda install mdanalysis

which will automatically install a full set of dependencies.

To upgrade later:

conda update mdanalysis

pip

Installation with pip and a minimal set of dependencies:

pip install --upgrade MDAnalysis

To install with a full set of dependencies (which includes everything needed for MDAnalysis.analysis), add the [analysis] tag:

pip install --upgrade MDAnalysis[analysis]

Tests

If you want to run the tests or use example files to follow some of the examples in the documentation or the tutorials, also install the MDAnalysisTests package:

conda install mdanalysistests            # with conda
pip install --upgrade MDAnalysisTests    # with pip

Source Code

Source code is available from https://github.com/MDAnalysis/mdanalysis/ under the GNU Public Licence, version 2. Obtain the sources with git.

git clone https://github.com/MDAnalysis/mdanalysis.git

The User Guide provides more information on how to install the development version of MDAnalysis.

Citation

When using MDAnalysis in published work, please cite [Michaud-Agrawal2011] and [Gowers2016].

MDAnalysis also contains specific algorithms and whole analysis modules whose algorithms have also been published in the scientific literature. Please make sure to also reference any Citations for included algorithms and modules in published work.

Thank you!

Indices and tables