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. Features include:
- Wide MD format support, including
pdb
,xtc
,trr
,dcd
,binpos
,netcdf
,mdcrd
,prmtop
, and more.- Extremely fast RMSD calculations (4x the speed of the original Theobald QCP).
- Extensive analysis functions including those that compute bonds, angles, dihedrals, hydrogen bonds, secondary structure, and NMR observables.
- Lightweight, Pythonic API.
MDTraj includes a command-line application, mdconvert
, for converting
trajectories between formats.
API Reference¶
Developing¶
Citation ¶
MDTraj is research software. If you make use of MDTraj in scientific publications, please cite it. The BibTeX reference is
@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}
}
License¶
MDTraj is licensed under the Lesser GNU General Public License (LGPL v2.1+).