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

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, ...)
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 user forums discourse.mdtraj.org.

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.

License

ProteinQure/mdtraj

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