<commit_before>#provide the full path of the protein PDB file
protein_pdb: CDK2_fixed_nohet.pdb

#provide the path to the ligand file with coordinates
ligand_file: CDK2_ligands.sdf

#The ligand file contains multiple ligands. Choose the indices of the ligands
#between which we should compute a relative free energy
old_ligand_index: 14
new_ligand_index: 15

#Provide the list of forcefield files. Non-standard files should
#be provided with a full path
forcefield_files:
    - gaff.xml
    - amber14/protein.ff14SB.xml
    - amber14/tip3p.xml

#the temperature and pressure of the simulation, as well as how much solvent paddding to add
#units:
#pressure: atm
#temperature: Kelvin
#padding: angstroms
pressure: 1.0
temperature: 300.0
solvent_padding: 9.0


#The name of the pickle file where we will save the setup object
save_setup_pickle_as: fesetup_hbonds.pkl

#the type of free energy calculation.
#currently, this could be either nonequilibrium or sams
fe_type: sams

#The number of SAMS states
n_states: 100

#the number of equilibration iterations:
n_equilibration_iterations: 10

#where to put the trajectories
trajectory_directory: cdk2_neq_hbonds<commit_msg>Add missing yaml file component<commit_after>#provide the full path of the protein PDB file
protein_pdb: CDK2_fixed_nohet.pdb

#provide the path to the ligand file with coordinates
ligand_file: CDK2_ligands.sdf

#The ligand file contains multiple ligands. Choose the indices of the ligands
#between which we should compute a relative free energy
old_ligand_index: 14
new_ligand_index: 15

#Provide the list of forcefield files. Non-standard files should
#be provided with a full path
forcefield_files:
    - gaff.xml
    - amber14/protein.ff14SB.xml
    - amber14/tip3p.xml

#the temperature and pressure of the simulation, as well as how much solvent paddding to add
#units:
#pressure: atm
#temperature: Kelvin
#padding: angstroms
pressure: 1.0
temperature: 300.0
solvent_padding: 9.0


#The name of the pickle file where we will save the setup object
save_setup_pickle_as: fesetup_hbonds.pkl

#the type of free energy calculation.
#currently, this could be either nonequilibrium or sams
fe_type: sams

#The number of SAMS states
n_states: 100

#the number of equilibration iterations:
n_equilibration_iterations: 10

#the number of equilibrium steps per iteration
n_equilibrium_steps_per_iteration: 1000

#where to put the trajectories
trajectory_directory: cdk2_neq_hbonds
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