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
  • Tutorial
    • 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
• Optimizing Lambda Schedules for Alchemical Free Energy Calculations
  • Learning objectives
  • Relevant literature
  • Tutorial Overview
  • Tutorial
    • 1. Introduction to Lambda Schedule Optimization
    • 2. Prerequisites and File Requirements
      • 2.1 Required Input Files
      • 2.2 Complete Energy Matrix Requirement
      • 2.3 Directory Organization
    • 3. Using fetkutils-tischedule.py
      • 3.1 Generate Optimized Schedule
      • 3.2 Predict the AR/PSO/KL Profile for Existing Schedule
    • 4. Analyzing Results
      • 4.1 Interpreting the Output File
• VMD Basics for Visualization
  • Learning Objectives
  • Tutorial
    • VMD
    • To Download and Install on your Local Computer:
    • Systems to Explore
    • Open VMD
    • Customizing Representations
    • Measuring Geometrical Properties
    • Selections with within and same
    • Hydrogen Bonding
    • Insepcting trajectories
    • Calculating Root-Mean-Square Deviation (RMSD)
    • RMSF Calculation
    • Image Rendering
• CPPTRAJ for Analysis
  • Learning Objectives
  • Tutorial
• TCL Scripting Basics
  • Learning Objectives
  • Tutorial
    • What is Tcl in VMD?
  • Using Tcl in the VMD TK Console
  • Atom Selections
  • Moving Atoms
  • Measuring distances
  • Calculating RMSD
  • Simple Visualization Example
• Writing a VMD TCL Script
  • Basic Script Structure
  • Running a TCL Script in VMD
    • Method 1 - From the Terminal
    • Method 2 - From the VMD TK Console
• Alchemical free energy calculations of pKa shifts in the MTR1 ribozyme
  • Learning objectives
  • Relevant literature
  • Introduction
  • Tutorial
    • 1. System setup
      • 1.1 Creating the complex state
      • 1.2 Creating the aqueous state
    • 1. Running the AFE Simulations
    • 3. Analyzing the results
    • 4. Applying the ACES method
    • 5. Comparing results with and without ACES