# 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`, `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` (renamed to `mdconvert-mdtraj` on Debian systems), 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` (`mdconvert-mdtraj`)

## 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+).