2026 Amber Workshop Activities

Welcome to the 2026 Amber Workshop Activities!

This workshop is taking place in Donostia, Basque Country, Spain from July 13th to July 17th, 2026.

For details and registration, see the workshop web page: 2026 Amber Workshop.

For the workshop, we have prepared a series of hands-on tutorials that will guide you through various aspects of using Amber for molecular simulations. These tutorials are designed to be interactive and will provide you with practical experience in setting up and running simulations, analyzing results, and understanding the underlying principles of molecular dynamics.

Some important information:

• Connect to the DIPC cluster using SSH. You will have received an email with your username and password. If you have not received this email, please contact the workshop organizers. Login as ssh <username>@hyperion.sw.ehu.es. You will be prompted for your password. If you have any issues with logging in, please contact the workshop organizers.

• The tutorials are designed to be run on the DIPC cluster. You will need to have access to the cluster and be able to log in using SSH. If you have any issues with accessing the cluster, please contact the workshop organizers.

• A few tutorials will include local jupyter notebooks that you can run on your own machine. The software VSCODE with the jupyter extension is recommended for running these notebooks. You can also use the jupyter notebook interface in your browser.

• The tutorials are organized by day and topic. Each tutorial will have a set of instructions and exercises that you can follow along with. You will also have the opportunity to ask questions and get help from the workshop instructors.

Day 1: Introduction to molecular simulations, visualization, and Amber

Open PDF for Lecture 1

Open PDF for Lecture 2

• Hands-On Session 1: Apply VMD and CPPTRAJ to visualize and analyze AMBER simulations

• Hands-On Session 2: Perform molecular dynamics (MD) simulations using AMBER

Day 2: Enzyme mechanisms: fine-tuned parameters, QM/MM, and free energy surfaces

Open PDF for Lecture 3

Open PDF for Lecture 4

Open PDF for Lecture 5

• Hands-On Session 3: Build an RNA enzyme (ribozyme) system containing 12-6-4 divalent ions and non-standard residues

• Hands-On Session 4: Perform umbrella sampling with QM/MM-ΔMLP and generate an FE surface using FE-ToolKit

• Hands-On Session 5: Perform SASM calculations to study catalytic mechanisms of a ribozyme

Day 3: Drug-like molecules: Generalized, bespoke and universal force fields

Open PDF for Lecture 6

Open PDF for Lecture 7

Open PDF for Lecture 8

• Hands-On Session 6: Generate force field parameters for drug-like molecules utilizing charge fitting procedures and the general Amber force field

• Hands-On Session 7: Create customized torsion corrections using the quantum deep potential interaction (QDπ) model and efficient wavefront approach

• Hands-On Session 8: Analyze AFE simulation results using FE-ToolKit

Day 4: Drug discovery: Modern alchemical free energy (AFE) methods

Open PDF for Lecture 9

Open PDF for Lecture 10

• Hands-On Session 9: Master the fundamentals of relative binding free energy calculations

• Hands-On Session 10: Master the fundamentals of absolute binding free energy calculations

Day 5: Machine learning models: Training accurate, robust, and efficient models for free energy predictions

Open PDF for Lecture 11

Open PDF for Lecture 12

Open PDF for Lecture 13

• Hands-On Session 11: Apply transfer learning and active learning strategies to optimize a foundational machine learning potential for improved accuracy on a specific target system

• Hands-On Session 12: Apply indirect AFE “book-ending” approach to efficiently correct low-level MM force field results to high-level QDπ

• Hands-On Session 13: Apply AmberStudio to perform high-throughput AFE simulations

Reference Materials

• AMBER and Molecular Simulation File Formats
  • Notes on Usage