MANIFEST

simple_model.m - run this to regenerate all simple model system results
plottmp.m - generate splitting probability comparison plots

run_muller_brown.m - script to generate trajectory on Mueller-Brown potential

integrate_bd.m - function to integrate Brownian dynamics trajectory 
committor_analysis.m - function to compute empirical committor from observed trajectory x_t

muller.m - Mueller 2D model potential
muller_brown.m - Mueller-Brown 2D model potential
rhee_pande.m - Rhee and Pande 2D model potential

plot_committor_analysis.m - function to plot committor analysis

best_hummer.m - perform Best-Hummer Bayesian analysis to compute PMF and diffusion constant, remapping observed coordinate to uniform diffusion constant

exportfig.m - utility for generating publication-quality figures

timeseries.java - Java support code for timeseries analysis