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. Extensive trajectory analysis routines are implemented. 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.
• Lightweight API, with a focus on speed and vectorized operations.

The library also ships with a flexible command-line application for converting trajectories between formats. When you install MDTraj, the script will be installed under the name mdconvert.

@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}
}