MDTraj: an open-source library for analysis of molecular dynamics trajectories

MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories and perform a variety of analyses, including fast RMSD, solvent accessible surface area, hydrogen bonding, etc. A highlight of MDTraj is the wide variety of molecular dynamics trajectory file formats which are supported, including RCSB pdb, GROMACS xtc, and trr, CHARMM / NAMD dcd, AMBER AMBER NetCDF, AMBER mdcrd, TINKER arc and MDTraj HDF5."

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

Features

With MDTraj, you can:

• Read and write from every MD format imaginable (pdb, xtc, trr, dcd, 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 documentation. To get involved, take a look at the GitHub issue tracker and/or the Discussions section.

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.

Project Status

MDTraj is actively maintained by community members and representatives from Folding@Home, The Molecular Sciences Software Institute, and Open Force Field Initiative. We welcome new users and contributors!

If you are interested in contributing, please check out the repository issue tracker. For feature ideas or general questions, please post in the repository discussions.