<commit_before># Path to protein file
protein_pdb: ripk2_receptor.pdb

# Path to ligand SDF file
ligand_file: ligands.sdf

# Indices of old and new ligands within SDF file
old_ligand_index: 0
new_ligand_index: 1

#
# Force fields
#

# OpenMM ffxml force field files installed via the openmm-forcefields package
# for biopolymers and solvents.
# Note that small molecule force field files should NOT be included here.
forcefield_files:
    - amber/ff14SB.xml # ff14SB protein force field
    - amber/tip3p_standard.xml # TIP3P and recommended monovalent ion parameters
    - amber/tip3p_HFE_multivalent.xml # for divalent ions
    - amber/phosaa10.xml # HANDLES THE TPO

# Small molecule force field
# Options include anything allowed by the openmmforcefields SystemGenerator
# e.g. one of ['openff-2.0.0', 'gaff-2.11']
small_molecule_forcefield: openff-2.0.0

#
# Simulation conditions
#

# Simulation setup options
solvent_padding: 9.0 # angstroms
pressure: 1 # atmsopheres
temperature: 300 # kelvin
timestep: 4 # femtoseconds

# Atom mapping specification
atom_expression:
  - IntType
bond_expession:
  - DefaultBonds

# Multi-state sampling scheme
# One of ['repex', 'nonequilibrium', 'sams']
fe_type: repex
checkpoint_interval: 50 # number of iterations

# Number of iterations to run
n_cycles: 5000

# Number of integration stpes per iteration
n_steps_per_move_application: 250

# Number of alchemical intermediate states to use
n_states: 12

# Number of equilibration iterations
n_equilibration_iterations: 0

# Location for storing trajectories
trajectory_directory: lig0to1
<commit_msg>document setting ionic strengh in example (#1104)<commit_after># Path to protein file
protein_pdb: ripk2_receptor.pdb

# Path to ligand SDF file
ligand_file: ligands.sdf

# Indices of old and new ligands within SDF file
old_ligand_index: 0
new_ligand_index: 1

#
# Force fields
#

# OpenMM ffxml force field files installed via the openmm-forcefields package
# for biopolymers and solvents.
# Note that small molecule force field files should NOT be included here.
forcefield_files:
    - amber/ff14SB.xml # ff14SB protein force field
    - amber/tip3p_standard.xml # TIP3P and recommended monovalent ion parameters
    - amber/tip3p_HFE_multivalent.xml # for divalent ions
    - amber/phosaa10.xml # HANDLES THE TPO

# Small molecule force field
# Options include anything allowed by the openmmforcefields SystemGenerator
# e.g. one of ['openff-2.0.0', 'gaff-2.11']
small_molecule_forcefield: openff-2.0.0

#
# Simulation conditions
#

# Simulation setup options
solvent_padding: 9.0 # angstroms
pressure: 1 # atmsopheres
temperature: 300 # kelvin
timestep: 4 # femtoseconds
ionic_strength: 0.15 # molar

# Atom mapping specification
atom_expression:
  - IntType
bond_expession:
  - DefaultBonds

# Multi-state sampling scheme
# One of ['repex', 'nonequilibrium', 'sams']
fe_type: repex
checkpoint_interval: 50 # number of iterations

# Number of iterations to run
n_cycles: 5000

# Number of integration stpes per iteration
n_steps_per_move_application: 250

# Number of alchemical intermediate states to use
n_states: 12

# Number of equilibration iterations
n_equilibration_iterations: 0

# Location for storing trajectories
trajectory_directory: lig0to1

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