Tutorials

Step-by-step guides for common workflows.

• Basic Protein Simulation
• Protein-Ligand Systems
• HPC Deployment with Parsl
• Analysis Workflows

Getting Started

Basic Protein Simulation

Complete walkthrough of building, running, and analyzing a simple protein simulation. Good starting point for new users.

Advanced Topics

Protein-Ligand Systems

Working with protein-ligand systems including small molecule parameterization with GAFF2.

HPC Deployment with Parsl

Deploying simulations on HPC clusters with Parsl, including configuration for PBS schedulers and GPU allocation.

Analysis Workflows

Comprehensive analysis pipelines combining multiple analysis tools for characterizing binding interfaces.