Explaining everything in this main directory:

init_equil: This is a standard diretory generated by CHARMM-GUI (with some files removed for size of directory friendliness) Before generating your string, you should equilibrate your structure with a short simulation. However, there is one more additional step you should take for this initial generation: Obtaining the colvar values for the first point of your string.

i.e. run the simulation with colvars ON but all force constants set to 0. In your colvars output file, you'll then get the values that you should set as your window for your very first window (This is quite important to get). In the directory you will see the example files that I used to run this initial simulation, and the averaging script (average_colvars.py) that I used to extract these colvar centers. You'll then take these average values and the equilibrated structure and move it in to the next directory where we generate the string.

generate_string: This is the directory where we actually make our string in a dielectric (for speed and efficiency). First need to run a simulation in the dielectric, and then use the averaging script to generate each subsequent window. More instructions are found in the generate_string directory

hydrate_string: This is the final step (before running REMD) where we actually hydrate our dielectric strings... This isn't quite done yet on the GitHub as of 1/18/19... I'll get to that at some time shortly (hopefully).