Welcome to the York Group’s Amber Tutorials

Getting Started

Welcome to the York Group’s Amber Tutorials!

Here you will find a collection of tutorials and guides designed to help you understand and utilize Amber to do state-of-the-art free energy and machine learning calculations.

Currently, we have three mains sections of tutorials:

1. Workshop Tutorials: These tutorials were created for the 2024 Amber Workshop and are designed to be self-contained, allowing you to follow along independently.

2. Internal Guides: These guides contain internal information and sample templates for creating new tutorials.

3. 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.

Contents

• Modular Tutorials
  • ForceField Tutorials
  • Alchemical Free Energy (AFE) Tutorials
  • Free Energy Surface Tutorials
  • Miscellaneous Tutorials
  • QM/MM Tutorials for MTR1
• Workshop Materials
  • 2024 Amber Workshop Tutorials
  • 2026 Amber Workshop Tutorials
• Internal guides
  • Template Tutorial (STEAL ME)
  • Installing Amber on Various Platforms
  • Getting Started in the York Lab
  • Getting Started with computers and Amber
  • Installing and Training with DeepMD-Kit
• In Progress Tutorials
  • Training a QM/MM+ΔMLP model with DeePMD-kit from AMBER simulation data
  • Learning to Run Absolute Binding Free Energy Calculations
  • Optimizing Lambda Schedules for Alchemical Free Energy Calculations
  • VMD Basics for Visualization
  • CPPTRAJ for Analysis
  • TCL Scripting Basics
  • Writing a VMD TCL Script
  • Alchemical free energy calculations of pKa shifts in the MTR1 ribozyme

Example Command Changes

You should see that these change when you change the drop down in the upper lefthand corner.

{{HOST}}

$ ssh user@..example..[this is plain text, normal code block]
# but for a host placeholder:
host: {{HOST}}
test: {{GAUSSIAN_LOAD}}

Note

Running on {{HOST}}