User Guide

• Introduction
  • Workflow overview
  • CLI Workflow
• Simulation Setup
  • Chemical Systems, Components and Thermodynamic Cycles
  • Creating Atom Mappings
  • Protocols in OpenFE
  • Defining the Ligand Network
  • Alchemical Networks: Planning a Simulation Campaign
• Execution
  • Execution with Quickrun
  • Parallel execution of repeats with Quickrun
  • Optimizing GPU performance with NVIDIA MPS
  • Protocols and the Execution Model Theory
• Results Gathering
  • Working with individual results
  • Working with networks of results
• CLI Interface
  • CLI basics
  • Customising CLI planning with YAML settings
• Details of Specific Protocols
  • Relative Hybrid Topology Protocol
  • Absolute Binding Protocol
  • Absolute Solvation Protocol
  • Separated Topologies Protocol
  • Plain MD Protocol
• Under the Hood
• Troubleshooting Simulations
  • Log Debug information
  • JAX warnings