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MDTraj: Molecular dynamics trajectory analysis in python

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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 involed, take a look at the github issue tracker and/or the user forums discourse.mdtraj.org.

License: LGPL 2.1+ Various sub-portions of this library may be individually distributed under different licenses. See those files for their specific terms.