Tutorials

Tutorials of GaMD Workshop 2024

The GaMD workshop will provide “hands-on” tutorial sessions different GaMD algorithms, including the GaMD, Ligand GaMD 3 (LiGaMD3) and Protein-Protein Interaction GaMD (PPI-GaMD).

Gaussian accelerated Molecular Dynamics (GaMD) Tutorial

Gaussian accelerated Molecular Dynamics (GaMD) is a biomolecular enhanced sampling method that works by adding a harmonic boost potential to smooth the system potential energy surface. This tutorial explains how you can perform GaMD simulations using the Amber24 simulation package. Alanine dipeptide is used as a model system for demonstration. You will learn how to run GaMD simulations to sample multiple conformational states of Alanine dipeptide in explicit solvent and reweight GaMD simulations to calculate the system free energy profiles. Knowledge about standard Molecular Dynamics (MD) simulations is required. Experiences with Amber and understanding of GaMD theory are preferred for learning the tutorial.

You can download the tutorial with the required simulation and analysis files in compressed tar.bz2 files at: GaMD-Tutorial-2024.pdf and GaMD.tar.bz2  (24.5MB)

Ligand Gaussian accelerated Molecular Dynamics 3 (GaMD3) Tutorial

This tutorial demonstrates how to use AMBER24+ and associated tools to perform and analyze LiGaMD3 simulations. The simulations can capture repetitive dissociation and binding of small molecules and flexible peptides, thereby exploring their binding mechanisms, thermodynamics and kinetics. Using host-guest binding of β-cyclodextrin and 1-butanol as a model system, we will demonstrate how to conduct LiGaMD3 simulations to capture ligand dissociation and rebinding. Additionally, we will demonstrate how to use the PyReweighting scripts to calculate 1D and 2D free energy landscapes and employ a 3D reweighting approach to predict ligand binding free energy. Prior knowledge of AMBER and basic Molecular Dynamics (MD) simulations is required.

You can download the tutorial with the required simulation and analysis files in compressed tar.bz2 files at: LiGaMD3-Tutorial-2024.pdf and LiGaMD3.tar.bz2 (33.7MB)

Protein-Protein Interaction Gaussian accelerated Molecular Dynamics (PPI-GaMD) Tutorial

Protein-Protein Interaction Gaussian accelerated Molecular Dynamics (PPI-GaMD) is a biomolecular enhanced sampling method that works by selectively boosting the interaction potential energy between protein partners to facilitate their slow dissociation, while another boost potential is applied to the remaining potential energy of the entire system to facilitate protein rebinding. This tutorial explains how you can perform PPI-GaMD simulations using the Amber24 simulation package. Barnase-barstar is used as a model system for demonstration. You will learn how to run PPI-GaMD simulations to sample multiple conformational states of barnase-barstar in explicit solvent and reweight PPI-GaMD simulations to calculate the system free energy profiles. Knowledge about standard Molecular Dynamics (MD) simulations is required. Experiences with Amber and understanding of PPI-GaMD theory are preferred for learning the tutorial.

You can download the tutorial with the required simulation and analysis files in compressed tar.bz2 files at: PPI-GaMD-2024.pdf and PPI-GaMD.tar.bz2 (16MB)