Supplementary Material for "Enhanced Sampling of Occluded Water Sites Using Nonequilibrium Candidate Monte Carlo"

This repository contains the data and scripts necessary to reproduce the results presented in our manuscript, "Enhanced Sampling of Occluded Water Sites Using Nonequilibrium Candidate Monte Carlo", by O. J. Melling, M. L. Samways, Y. Ge, D. Mobley and J. W. Essex (2022).

There are separate directories for the bulk water simulations as well as the three protein-ligand test systems: MUP-I, HSP90 and trypsin with the scripts and input files required to run GCMC/MD, GCNCMC/MD and water hopping simulations. There is also an analysis/ directory with the necessary scripts to perform clustering analysis and generation of electrond density maps from the simulation trajectories. More information on how to perform the simulations and analysis can be found within each directory. The grand module required to run these simulations can be downloaded here.

If you encounter any problems with these scripts, please contact the authors.