# Set the general options of our simulation
options:
  minimize: yes
  verbose: yes
  temperature: 300*kelvin
  pressure: 1*atmosphere # To run with NVT ensemble, set this option to "null". Defaults to 1 atm if excluded
  platform: CUDA
  output_dir: yank_output_separated
  checkpoint_interval: 10
  default_number_of_iterations: 100000
  default_nsteps_per_iteration: 500
  constraints: HBonds
  default_timestep: 2.0 * femtosecond
  equilibration_timestep: 1.0 * femtosecond
  resume_simulation: yes

# Define the solvent for our system, here we use Particle Mesh Ewald for long range interactions
solvents:
  # We can title this solvent whatever we want. We just call it "pme" for easy remembering
  pme:
    nonbonded_method: PME # Main definition of the nonbonded method
    nonbonded_cutoff: 11*angstroms # Cutoff between short- and long-range interactions

# Define the systems: What is the ligand, receptor, and solvent we put them in
systems:
  # We can call our system anything we want, this example just uses a short name for the receptor hyphenated with the ligand
  protein_ligand:
    phase1_path: [system_complex.pdb, system_complex.xml]
    phase2_path: [system_solvent.pdb, system_solvent.xml]
    ligand_dsl: resname=~"19"

# The protocols define the alchemical path each phase will take, we use the same lambda values, though they could be different
protocols:
  # Call the protocol whatever you would like, here we name it based on the type of calculation we are running
  absolute-binding:
    complex:
      alchemical_path:
        lambda_electrostatics: [0.00]
        lambda_sterics:        [0.00]
        # Set lambda restraints reverse of coupling parameter (see below in "restraint" for reason)
        lambda_restraints:     [1.00]
    solvent:
      alchemical_path:
        lambda_electrostatics: [0.00]
        lambda_sterics:        [0.00]

# Here we combine the system and the protocol to make an experiment
experiments:
  system: protein_ligand
  protocol: absolute-binding
  restraint:
    type: Harmonic # Keep the ligand near the protein
    # We set a harmonic restraint which biases the ligand to remain close to the receptor when it is decoupled
    # to prevent it from drifting into the whole box and possibly never visiting the binidng site again.
    # The Harmonic restraint is fairly weak since it restrains a single ligand atom to the centroid-most receptor atom,
    # which may or may not be a binding site.
    # The restraint is opposite the coupling parameter since we want the ligand unrestrained in the binding site
    # We correct for the free energy of this restraint through the `standard_state_correction` calculated automatically.