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Tutorials

Welcome to the PRISM tutorials! These hands-on guides will walk you through common workflows and best practices for building and analyzing protein-ligand MD systems.

Available Tutorials

Basic Tutorial

Level: Beginner Time: 30-60 minutes Topics: System building, running simulations, basic analysis

Learn the fundamentals of PRISM by building a simple protein-ligand system from start to finish. This tutorial covers the complete workflow from input preparation to trajectory analysis.

What you'll learn: - Preparing protein and ligand inputs - Building an MD system with default settings - Running equilibration and production simulations - Analyzing protein-ligand interactions - Visualizing results

Force Field Selection Tutorial

Level: Intermediate Time: 45-90 minutes Topics: Multiple force fields, comparison, validation

Explore PRISM's support for 8+ ligand force fields. Learn how to choose the right force field for your system and compare results across different parameterization methods.

What you'll learn: - When to use GAFF vs OpenFF vs OPLS-AA - Building the same system with multiple force fields - Comparing binding energies and structural stability - Validating force field quality - Best practices for force field selection

PMF Calculation Workflow

Level: Advanced Time: 2-4 hours (+ computation time) Topics: Binding free energy, PMF, umbrella sampling

Complete walkthrough of calculating protein-ligand binding free energies using umbrella sampling and WHAM analysis.

What you'll learn: - Setting up PMF calculations - Running steered MD and umbrella sampling - Analyzing PMF profiles with WHAM - Calculating binding free energies - Troubleshooting common PMF issues

Batch Processing Tutorial

Level: Intermediate Time: 60-90 minutes Topics: High-throughput, automation, parallel processing

Learn how to process multiple protein-ligand complexes efficiently using PRISM's Python API and cluster resources.

What you'll learn: - Automating system building for multiple ligands - Submitting batch jobs to compute clusters - Processing results from multiple simulations - Creating comparison reports - Best practices for high-throughput screening

Tutorial Prerequisites

Required Software

All tutorials assume you have:

  • PRISM installed and configured (Installation Guide)
  • GROMACS 2020.x or newer
  • Python 3.8+
  • Basic command-line familiarity

Optional Software

Some tutorials may benefit from:

  • MDTraj (for advanced analysis)
  • RDKit (for ligand handling)
  • Jupyter notebooks (for interactive analysis)

Sample Data

Download tutorial data:

# Clone the PRISM tutorial data repository
git clone https://github.com/AIB001/PRISM-tutorial-data.git
cd PRISM-tutorial-data

# Or download specific tutorial datasets
wget https://github.com/AIB001/PRISM-tutorial-data/raw/main/basic_tutorial.tar.gz
tar -xzf basic_tutorial.tar.gz

Learning Path

graph TD
    A[Start Here] --> B[Basic Tutorial]
    B --> C{What's your goal?}
    C -->|Multiple ligands| D[Force Field Tutorial]
    C -->|Binding energy| E[PMF Tutorial]
    C -->|High-throughput| F[Batch Tutorial]
    D --> G[Advanced Topics]
    E --> G
    F --> G

For Beginners

  1. Start with the Basic Tutorial
  2. Review the User Guide for deeper understanding
  3. Try the Force Field Tutorial to explore options

For Intermediate Users

  1. Complete the Force Field Tutorial
  2. Learn Batch Processing for efficiency
  3. Explore Examples for specific use cases

For Advanced Users

  1. Master PMF Calculations
  2. Study the API Reference for custom workflows
  3. Contribute your own examples!

Tutorial Format

Each tutorial follows this structure:

  • Objectives: What you'll accomplish
  • Prerequisites: What you need before starting
  • Step-by-step instructions: Detailed walkthrough
  • Expected output: What results to expect
  • Troubleshooting: Common issues and solutions
  • Next steps: Where to go from here

Getting Help

If you encounter issues while following tutorials:

  1. Check the Troubleshooting Guide
  2. Review error messages carefully - they often indicate the problem
  3. Verify dependencies are installed (see Installation)
  4. Ask for help:
  5. GitHub Issues: AIB001/PRISM
  6. Email: zhaoqi.shi@wisc.edu

Contributing Tutorials

Have a useful workflow or case study to share? We welcome tutorial contributions!

To contribute:

  1. Fork the PRISM-Tutorial repository
  2. Add your tutorial following our format
  3. Include sample data if needed
  4. Submit a pull request

Good tutorial topics include:

  • Specific protein families (kinases, GPCRs, etc.)
  • Special cases (metal-binding, covalent inhibitors)
  • Integration with other tools
  • Advanced analysis techniques
  • Optimization strategies

Additional Resources

What's Next