MDAnalysis is a Python library to analyze molecular dynamics trajectories.
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MDAnalysis Repository README

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MDAnalysis is a Python toolkit to analyze molecular dynamics trajectories generated by a wide range of popular simulation packages including DL_Poly, CHARMM, Amber, NAMD, LAMMPS, and Gromacs. (See the lists of supported trajectory formats and topology formats.)

import MDAnalysis as mda

# Load simulation results with a single line
u = mda.Universe('topol.tpr','traj.trr')

# Select atoms
ag = u.select_atoms('name OH')

# Atom data made available as Numpy arrays

# Iterate through trajectories
for ts in u.trajectory:
    print ag.center_of_mass()

Source code

Source code is hosted in a git repository at

and is available under the GNU General Public License, version 2 (see the file LICENSE).

This is the top level of the master repository. It contains

  1. the MDAnalysis toolkit source files in the directory

  2. the unit tests together with any input files required for running those tests in the directory


The directory maintainer contains scripts only needed for maintaining releases and are not generally useful for the user or the typical developer. The vm directory contains configurations for virtual machines.

(For more details on the directory layout see Issue 87 on the MDAnalysis issue tracker.)

[*]build: Unit testing is for the whole package; coverage is shown for the core library modules (which excludes MDAnalysis.analysis and MDAnalysis.visualization at the moment). For more details and discussion see issue #286.