Matlab files to produce figures appearing in:

Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments 
John D. Chodera and Vijay S. Pande. 
Phys. Rev. Lett., 107:098102 (2011)

Written by:

John D. Chodera
jchodera@berkeley.edu
University of California, Berkeley

See COPYRIGHT.txt for copyright notice applying to all software in this distribution.

* Rhee-Pande model:

generate_model_trajectory.m - generate trajectory for simple model
generate_model_plots.m - generate plots for simple model


* DNA hairpin from Block lab:

generate_hairpin_plots.m - read DNA hairpin data and generate Best-Hummer plot
analyze_hairpin_data.m - perform splitting analysis on hairpin data
plot_hairpin_trajectory.m - plot splitting for DNA hairpin trajectory.

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* Support scripts and Java code used by the above driver scripts:

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 - perform committor analysis and generate detailed plot, including histogram, PMF, and trajectory
plot_committor_only.m - perform committor analysis and generate committor plot only

best_hummer.m - perform Best-Hummer Bayesian analysis to compute PMF and diffusion constant, remapping observed coordinate to uniform diffusion constant
rate_matrix_guess.m - guess initial rate matrix using optimization
hummer_rate_matrix_update.m - perform Hummer Bayesian rate matrix sampling

timeseries.java - Java support code for timeseries analysis
bayesian.java - Java support code for Best-Hummer Bayesian analysis scheme

* Redistributed for convenience (see license notice in those directories)

exportfig/ - Matlab package to handle figure exports
epsmerge/ - Matlab package to handle figure merging