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 {
	author = {McGibbon, Robert T. and Beauchamp, Kyle A. and Schwantes, Christian R. and Wang, Lee-Ping and Hern{\'a}ndez, Carlos X. and Harrigan, Matthew P. and Lane, Thomas J. and Swails, Jason M. and Pande, Vijay S.},
	title = {MDTraj: a modern, open library for the analysis of molecular dynamics trajectories},
	year = {2014},
	doi = {10.1101/008896},
	publisher = {Cold Spring Harbor Labs Journals},
	journal = {bioRxiv}
}

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.