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.
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}
}
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.