- examples
- setup: collection of directories for learning how to set up and run simulations.
- analysis: example notebooks for analyzing simulations
- protocols
- install: protocol for installing required software and preparing environment
- run-a-simulation: protocol for setting up and running a simulation
- generate-custom-molecule-parameters: protocol for generating parameters using charmm-gui
- setup_md: helper program, input files, and forcefield
- ligand_param: pre-generated ligand parameters for some molecules of interest
- test-materials: directory holding scripts and files to make sure the environment is configured correctly.