WHAM_BB_TWOD version 0.1                                

  Introduction

The free energy (or the potential of mean force) along a set of reaction
coordinates is a central quantity in computational chemistry.  Umbrella sampling
combined with weighted histogram analysis method (WHAM) is a powerful tool 
for
such calculation.  Here, I have provided a set of programs to perform WHAM with
Bayesian bootstrapping. The source code for these programs is available for
free under a general public license (GPL).  I referred to David Minh's MATLAB
code while writing it.  


  Installation

The package contains the following contents:
1. wham_bb_twoD binary for Mac OSX
2. its C++ source code and Makefile
3. Three sample python scripts: 
master_input.py and hist_twoD.py prepare the input files for wham_bb_twoD 
master_run.py performs multiple WHAM analysis to get an error estimate using
Bayesian bootstrapping.  

These three python scripts were written specifically for my own research
project, but it should be fairly easy to change them to fit your own research
purpose.  You can also re-write them in your preferred language.  In the future,
I will develop a general-purpose script to prepare these input files. 

To compile the source code with g++ in Mac OSX or Linux, simply type make.  

Feel free to send comments and suggestions to:
ll@molbio.mgh.harvard.edu


  References

 An excellent introduction to umbrella sampling can be found in 
 Introduction to modern statistical mechanics
 David Chandler

 A great reference for the theoretical background of WHAM is 
 The calculation of the potential of mean force using computer simulations
 Benoit Roux
 Computer Physics Communication 91, 275-282 (1995)

 The error of the WHAM free energy calculation can be estimated by 
 Bayesian bootstrapping.  This is based on:
 g_wham--a free weighted histogram analysis implementation including robust 
error 
 and autocorrelation estimates
 Jochen S. Hub, Bert L. de Groot, and David van der Spoel
 J. Chem. Theory Comp. 6, 3713-3720 (2010)

 The code was developed on the basis of David Minh's MATLAB code for 
 one-dimensional WHAM.
 Optimized free energies from bidirectional single-molecule force spectroscopy. 
 D. Minh and A. Adib. 
 Physical Review Letters 100, 180602 (2008).