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 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.

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

    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}


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