Files and scripts used to set up MD simulations in the Harms Lab

• 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.