Introduction
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Milestoning sampling protocol to calculate free energy and kinetics of rare events.

Please cite W. Ma and K. Schulten. JACS, 137: 3031. (2015) in publications reporting results obtained with this package.
For more details about the theoretical backgrouds, please check the supporting information in the above publication.


Description of main codes
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run_milestoning.sh - Script to launch the milestoning simulations on a supercomputuer.

make_files_ms.sh - Script to set up necessary files for simulations

milestoning_VT.namd - NAMD configuration file providing simulation parameters.

soft_wall.tcl - Code to perform milestoning with Voronoi Tessellation using soft-wall restraint potentials. 

cal_MFPT.py - Script to compute the free energy profile and the mean first passage times from one milestone to another one.


Instructions
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a. One has to first obtain the center conformations of each Voronoi cell. This can be done with the string method.
   See http://www.ks.uiuc.edu/~wenma/codes/string_method/ for details (the colvars constraint files harmonic_*.config
   can also be obtained there). 
   
b. Use make_files_ms.sh to set up the files required for simulations. It also calls a script (set_index.tcl)
   to create an index file for atoms used for reaction coordinates in milestoning.
   
c. Use run_milestoning.sh to launch simulations on supercomputers. The script replica_ms.sh is called to
   allocate computational resources (a sample for XSEDE's Stampede is provided).
   
d. Script cal_MFPT.py can be used to obtain the free energy profile and the mean first passage times from one
   milestone to another one. Related output files are 'Free_energy.dat' and 'main_MFPTs.dat'.


Getting Help
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Email address of the author: wenma2@illinois.edu