Introduction
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This document provides the details of scripts implementing the string method with swarm-of-trajectories with NAMD.

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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string.sh	script to launch string method calculations on clusters

multifit.py	code to perform multi-dimensional curve fitting during string reparameterization

swarm.namd	NAMD configuration file for running swarms of trajectories

NVT.namd	NAMD configuration file for running restraint simulations to equilibrate the systems 
         	for each image after obtaining an updated string


Instructions
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(1) Modify key parameters in string.sh, such as number of images in the string and number of trajectories 
    in a swarm.

(2) Use script mk_swarm_input.sh to generate NAMD input files for swarms-of-trajectories simulations.

(3) Use string.sh to launch string simulations on clusters or supercomputers until the calculation converages.

(4) Key outputs include Free_energy.dat (free energy profile along the string) and ave.*.pdb 
    (averaged protein coordinates representing each image along the string)


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