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 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.

• Installation
• New to Python
• Examples
• What’s New?

API Reference

• Trajectory Reference
• Analysis Reference
• Atom Selection Reference
• Low-level API
• OpenMM Reporters
• MDTraj Utils
• mdconvert

Developing

• MDTraj HDF5 Format Specification

Citation

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+).