Simulation Setup

This section provides details on how to set up free energy calculation or MD simulations.

All protocols in OpenFE follow the same general structure:

• Reading in input structures and Creating ChemicalSystem s

• Defining the Protocol with specific ProtocolSettings

• Creating LigandAtomMapping s for relative free energy calculations Protocols

The image below demonstrates how, for relative free energy calculations, you plan a network of ligand transformations starting from input SDF / MOL2 / PDB files:

The procedure for setting up a simulation depends somewhat on the on the type of free energy calculation you are running. See more detailed instructions can be found under:

• ChemicalSystems, Components and Thermodynamic Cycles
  • Chemical Systems
  • Components
  • Thermodynamic Cycles
  • See Also
• Creating Atom Mappings
  • Generating Mappings
  • Visualising Mappings
  • Scoring Mappings
• Creating and using Protocols
  • Settings and creating Protocols
  • Using Protocols
• Defining the Ligand Network
  • Generating Ligand Networks
• Alchemical Networks: Planning a Simulation Campaign
  • See Also
• Alchemical Networks: Creation
  • Python API
  • Alchemical Network Planners
  • Command-line interface

If you intend to set up your alchemical network using the Python interface, but to run it using the CLI, you will want to export the network in the same format used by the CLI. See dumping transformations for more details.