This library supports the reading and writing of molecular dynamics trajectories in a variety of formats. Currently, there is full support for PDB, DCD, XTC, TRR, binpos, AMBER NetCDF, AMBER mdcrd, and MDTraj HDF5. There is partial support for the TINKER arc format (only reading).

MDTraj is structured around a convent numpy-based Trajectory object. Its RMSD (optimal cartesian root-mean-square deviation) library gives you access to fast parallel SSE3-based structural deviations using the quaternion characteristic polynomial (Theobald QCP) method at 4x the speed of the original Theobald code and over 3x as fast as Theobald code modified to use GotoBLAS.

For details, see the documentation.

MDtraj is free software; you can redistribute it and/or modify it under the
terms of the GNU Lesser General Public License as published by the Free
Software Foundation; either version 2.1 of the License, or (at your option)
any later version.

This library is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
details. You should have received a copy of the GNU Lesser General Public
License along with this Module; if not, see <http://www.gnu.org/licenses/>.

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