/mdtraj

A modern, open library for the analysis of molecular dynamics trajectories

Primary LanguagePythonGNU Lesser General Public License v2.1LGPL-2.1

MDTraj: a modern, open library for the analysis of molecular dynamics trajectories

Build Status PyPI Version Anaconda-Server Version Anaconda-Server Downloads DOI for Citing MDTraj

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

With MDTraj, you can

  • Read and write from every MD format imaginable (pdb, xtc, trr, dcd, binpos, netcdf, mdcrd, prmtop, gsd, ...)
  • Run blazingly fast RMSD calculations (4x the speed of the original Theobald QCP).
  • Use tons of analysis functions like bonds/angles/dihedrals, hydrogen bonding identification, secondary structure assignment, NMR observables.
  • Use a lightweight API, with a focus on speed and vectorized operations.

For details, see the website at mdtraj.org. To get involved, take a look at the github issue tracker and/or the gitter room.

Citation

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

@article{McGibbon2015MDTraj,
    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.},
    title = {MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories},
    journal = {Biophysical Journal},
    volume = {109},
    number = {8},
    pages = {1528 -- 1532},
    year = {2015},
    doi = {10.1016/j.bpj.2015.08.015}
}

License

GNU LGPL version 2.1, or at your option a later version of the license. Various sub-portions of this library may be independently distributed under different licenses. See those files for their specific terms.

Contributing

If you'd like to contribute to mdtraj you're most welcome! It’s people like you who make it such a great tool. Generally, the library is mostly in "maintenance mode" -- we are not specifically planning to add major new features. Bug-fixes, additional testing and documentation, and small features that integrate well with the existing library are most appreciated!