cclauss / mdtraj Goto Github PK

Hi there!

MDTraj is a project that I (@rmcgibbo) primarily developed between 2013 and 2016 while I was a graduate student. That was a long time ago! I've moved on, and no longer use MDTraj in my current role. Most of the other contributors from that time have similarly moved on. I do respond to github issues and pull requests from time to time, but my bandwidth is limited so don't expect to necessarily get a response on github issues from me. (Also please don't email me with support requests).

MDTraj is looking for new maintainers! I would be happy to transfer ownership and responsibility of the code base to another group of maintainers. Please reach out to me if you're interested in taking over the project.

Best,

Robert T. McGibbon (@rmcgibbo)

May 2, 2022

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, gsd, ...)
• 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 gitter room.

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.