Tutorial 1 features running simulations on a model system constructed from two PDB structures, where one structure contains the protein-ligand complex and the other is an apo-structure of the homolog to be simulated. This tutorial familiarizes the user with basic PyMOL operations such as atom selection, addition of hydrogens to the ligand and deletion of undesirable co-crystallized molecules required prior to running an MD simulation. Tutorial 2 shows how to include a common co-factor (NADPH) alongside a ligand. The parameters and topology for NADPH are also provided on the tutorial webpage (along with their original source).