York Group Workshop Materials

Welcome to the York Group’s Workshop Tutorials!

These are collections of tutorials that have been used for past workshops, and have been left in the final state from that workshop.

Workshop Tutorials

• 2024 Amber Workshop Tutorials
  • VMD and CPPTRAJ Basics for Visualization and Analysis of MD Trajectories
  • Simulating the MTR1 ribozyme
  • Preparing a Small Molecule from PDB to Simulation
  • Parameterizing a non-standard residue for the MTR1 ribozyme
  • Building and Simulating TYK2 Protein Ligand System
  • Reaction Free Energy Profiles from QM/MM simulations: Methyl Transfer reaction in MTR1
  • Absolute Solvation Free Energy using ACES
  • Relative Binding Free Energy using ACES
  • QM/MM+ΔMLP simulations of the MTR1 ribozyme
  • MM-to-QM/MM Free Energy “Bookend” Corrections using GFN2-xTB and QDπ2 machine learning potential.