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MDTraj

Read, write and analyze MD trajectories with only a few lines of Python code.

MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories. Features include:

  • Wide MD format support, including pdb, xtc, trr, dcd, binpos, netcdf, mdcrd, prmtop, and more.
  • Extremely fast RMSD calculations (4x the speed of the original Theobald QCP).
  • Extensive :ref:`analysis <analysis>` functions including those that compute bonds, angles, dihedrals, hydrogen bonds, secondary structure, and NMR observables.
  • Lightweight, Pythonic API.

MDTraj includes a command-line application, mdconvert, for converting trajectories between formats.

.. toctree::
   :maxdepth: 1

   installation
   new_to_python
   examples/index
   whatsnew

API Reference

.. toctree::
   :maxdepth: 1

   load_functions
   analysis
   atom_selection
   api/trajectory_files
   api/reporters
   api/utils
   mdconvert


Developing

.. toctree::
   :maxdepth: 1

   hdf5_format



Citation DOI for Citing MDTraj

MDTraj is research software. If you make use of MDTraj in scientific publications, please cite it. The BibTeX reference is

@article{McGibbon2015MDTraj,
    title = {MDTraj: A Modern Open Library for the Analysis of
    Molecular Dynamics Trajectories},
    author = {McGibbon, Robert T. and Beauchamp, Kyle A. and Harrigan,
    Matthew P. and Klein, Christoph and Swails, Jason M. and
    Hern{\'a}ndez, Carlos X.  and Schwantes, Christian R. and Wang,
    Lee-Ping and Lane, Thomas J. and Pande, Vijay S.},
    journal = {Biophysical Journal},
    volume = {109},
    number = {8},
    pages = {1528 -- 1532},
    year = {2015},
    doi = {10.1016/j.bpj.2015.08.015}
}

License

MDTraj is licensed under the Lesser GNU General Public License (LGPL v2.1+).