# Example illustrating the application of MBAR to compute a 1D PMF from an umbrella sampling simulation.

The data represents an umbrella sampling simulation for the chi torsion of a valine sidechain in lysozyme L99A with benzene bound in the cavity.

# Reference

D. L. Mobley, A. P. Graves, J. D. Chodera, A. C. McReynolds, B. K. Shoichet and K. A. Dill, "Predicting absolute ligand binding free energies to a simple model site," Journal of Molecular Biology 371(4):1118-1134 (2007).
http://dx.doi.org/10.1016/j.jmb.2007.06.002

# Usage

Run the included `umbrella-sampling.py` code.  `umbrella-sampling.sample_output` gives the expected output of the program.

The code `umbrella-sampling-advaced-pmf.py` demonstrates significant additional functionality (in beta), but takes significantly longer to run.
