In Progress Tutorials

Welcome to the York Group’s In Progress Tutorials!

These tutorials are currently being developed and refined, and are likely not what you want to be using to learn. However, if you are interested in seeing what is coming soon, feel free to explore these in-progress tutorials.

In Progress Tutorials

• Training a QM/MM+ΔMLP model with DeePMD-kit from AMBER simulation data
  • Learning objectives
  • Relevant literature
  • Introduction
  • Outline
  • 1. Preparing training data from AMBER QM/MM simulations
    • 1.1 String simulations
    • 1.2 Production simulations
    • 1.3 Single point calculations
    • 1.4 Packaging the data
  • 2. Training a QM/MM+ΔMLP model with DeePMD-kit
    • 2.1 Generating input files for a Deep Potential
    • 2.2 Generating input files for MACE
    • 2.3 Machine files
    • 2.4 Running DP-GEN simplify
    • 2.5 Starting from a pretrained model
    • 2.6 Evaluating a model
  • 3. Training a QM/MM+ΔMLP model with DeePMD-kit
    • 3.1 QM/MM+ΔMLP simulations
• Creating Bespoke Force-Field Parameters
  • Learning objectives
  • Relevant literature
  • Outline
  • Tutorial
    • Overview of Ligand Parameterization and Terminology
    • Parameterizing with LigandParam
    • Installation
    • Linear Dihedral Scans
    • WaveFront Dihedral Scans
    • Dihedral Fitting with FFPOPT