Repository containing setup and analysis scripts used in the paper studying the high-energy water in cucurbit[8]uril.
NOTE: This repo is still a work in progress, there are still many things I will add in the near future.
The main functions that converts/creates the hard sphere model of a dummy particle is in hard_sphere.py.
The file create_hard-sphere.py creates an OpenMM System XML file containing the modified potentials after loading the AMBER files *.prmtop and *.rst7
TODO: Add a script that runs the simulations (with and without umbrella sampling restraints) and the alchemical version that was used to estiamte the hydration free energy.