Simulation Setup

This section provides details on how to set up a free energy calculation. This will get you from your SDF/MOL2/PDB files to an AlchemicalNetwork, which contains all the information to run a simulation campaign.

The first thing you will need to do will be to load in your molecules. OpenFE can small molecules from anything that RDKit can handle, and can load proteins from PDB or PDBx. For details of this, see ref:???.

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:

• Defining RBFE Calculations
• Defining RHFE/RSFE Calculations

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 ??? for details on that. .. TODO link to docs on outputting the network