MDAnalysis Repository README
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 ag.positions ag.velocities ag.forces # Iterate through trajectories for ts in u.trajectory: print(ag.center_of_mass())
There are also a number of tutorials on the MDAnalysis homepage that explain how to conduct RMSD calculations, Alignment and more features of MDAnalysis.
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
the MDAnalysis toolkit source files in the directory
the unit tests together with any input files required for running those tests in the directory
maintainer contains scripts only needed for
maintaining releases and are not generally useful for the user or the
(For more details on the directory layout see Issue 87 on the MDAnalysis issue tracker.)
Guide for Developers
To setup a development environment and run the testsuite you can use this guide. If you are a new developer who would like to start contributing to MDAnalysis as a start you can increase our code coverage, the guides explain how to find uncovered code.
|[*]||build: Unit testing is for the whole package; coverage is shown for the core library modules and the analysis modules.|