Analysis of particle diffusion in molecular dynamics simulations

Contains Python utility functions for the analysis of diffusion in molecular dynamics simulation trajectories.

The documentation for the project is available here: http://diffusion-analysis-md-simulations.readthedocs.org/en/latest/index.html

An IPython notebook containing an example diffusion calculation is available: https://github.com/tylerjereddy/diffusion_analysis_MD_simulations/blob/master/diffusion_analysis_sim126_extended.ipynb

Please cite:

And even better if you cite the original paper: Reddy et al. (2015) Structure 23: 584-97. [DOI]

For contributions:

• ensure all unit tests pass (run pytest)
• ensure all doctests pass (run doctesting.py)
• if you import new modules, you may need to mock them in the Sphinx conf.py documentation file so that the docs are properly compiled by readthedocs
• attempt to match the numpy documentation standard as closely as possible