A modern, open library for the analysis of molecular dynamics trajectories
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marscher Merge pull request #1392 from sunhwan/master
allow RMSD calls when ref_atom_indices and atom_indices are used
Latest commit e26ca71 Dec 6, 2018


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

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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 DOI for Citing MDTraj

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

    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}


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.