Workshop Materials

Welcome to the York Group’s Workshop Activities!

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

Workshop Activities

• 2024 Amber Workshop Activities
  • 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.
• 2026 Amber Workshop Activities
  • Day 1: Introduction to molecular simulations, visualization, and Amber
  • Day 2: Enzyme mechanisms: fine-tuned parameters, QM/MM, and free energy surfaces
  • Day 3: Drug-like molecules: Generalized, bespoke and universal force fields
  • Day 4: Drug discovery: Modern alchemical free energy (AFE) methods
  • Day 5: Machine learning models: Training accurate, robust, and efficient models for free energy predictions