================================ MDAnalysis Repository README

|build| |cov| [*]_

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

.. code:: python

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

ag.positions ag.velocities ag.forces

Iterate through trajectories

for ts in u.trajectory: print(ag.center_of_mass())

Source code

Source code is hosted in a git repository at

https://github.com/MDAnalysis/mdanalysis

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

the MDAnalysis toolkit source files in the directory ::

package/
the unit tests together with any input files required for running those tests in the directory ::

testsuite/

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.)

.. Footnotes

.. [*] build: Unit testing is for the whole package; coverage is shown for the core library modules and the analysis modules (which excludes MDAnalysis.visualization_ at the moment).

.. _trajectory formats: http://docs.mdanalysis.org/documentation_pages/coordinates/init.html#id1 .. _topology formats: http://docs.mdanalysis.org/documentation_pages/topology/init.html#supported-topology-formats .. _Issue 87: https://github.com/MDAnalysis/mdanalysis/issues/87 .. _MDAnalysis: http://www.mdanalysis.org .. LICENSE: https://github.com/MDAnalysis/mdanalysis/blob/master/LICENSE .. #286: https://github.com/MDAnalysis/mdanalysis/issues/286 .. _MDAnalysis.analysis: http://docs.mdanalysis.org/documentation_pages/analysis_modules.html .. _MDAnalysis.visualization: http://docs.mdanalysis.org/documentation_pages/visualization_modules.html

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