docs/yank-yaml-cookbook/all-options.yaml
# Here are listed all the options that is possible to specify in a
# Yank YAML script. There are no mandatory options. If not specified,
# an option assumes the default value listed below.
---
options:
# GENERAL OPTIONS
# ---------------
verbose: no # Turn on/off verbose output.
resume_setup: no # By default, Yank will raise an error when it detects
resume_simulation: no # that it will have to overwrite an existing file. Set
# resume_setup and/or resume_simulation if you want Yank
# to resume from an existing setup (molecules and system
# files) and/or simulation (netcdf4 trajectory files)
# respectively instead.
output_dir: output # The main output folder. A relative path is interpreted
# as relative w.r.t. the YAML script path.
setup_dir: setup # The main folder where the setup and simulation files
experiments_dir: experiments # are saved. Relative paths are interpreted as relative
# w.r.t. output_dir path.
platform: fastest # The OpenMM platform to use between 'Reference', 'CPU',
# 'OpenCL', and 'CUDA'. The default value 'fastest' selects
# automatically the fastest available platform.
precision: auto # Precision mode. For OpenCL and CUDA platforms, this
# can be set to 'single', 'mixed' or 'double'. The default
# value 'auto' selects always 'mixed' when the device
# support this precision, otherwise 'single'.
# SYSTEM AND SIMULATION PREPARATION
# ---------------------------------
randomize_ligand: no # Randomize the position of the ligand before starting the
randomize_ligand_sigma_multiplier: 2.0 # simulation. This works only in implicit solvent. The
randomize_ligand_close_cutoff: 1.5 * angstrom # ligand will be randomly rotated and displaced by a vector
# with magnitude proportional to randomize_ligand_sigma_multiplier
# with the constraint of being at a distance greater than
# randomize_ligand_close_cutoff from the receptor.
temperature: 298.0 * kelvin # Temperature of the system.
pressure: 1.0 * atmosphere # Pressure of the system. Set to null for NVT ensemble.
hydrogen_mass: 1.0 * amu # Hydrogen mass for HMR simulations.
constraints: HBonds # Constrain bond lengths and angles. Possible values are null,
# HBonds, AllBonds, and HAngles (see Openmm createSystem()).
# SIMULATION PARAMETERS
# ---------------------
online_analysis: no # If set, analysis will occur each iteration.
online_analysis_min_iterations: 20 # Minimum number of iterations needed to begin online analysis.
show_energies: yes # If True, will print energies at each iteration.
show_mixing_statistics: yes # If True, will show mixing statistics at each iteration.
minimize: yes # Minimize configurations before running the simulation.
minimize_max_iterations: 0 # Maximum number of iterations for minimization.
minimize_tolerance: 1.0 * kilojoules_per_mole / nanometers # Set minimization tolerance.
number_of_equilibration_iterations: 1 # Number of equilibration iterations.
equilibration_timestep: 1.0 * femtosecond # Timestep for use in equilibration.
default_number_of_iterations: 1 # The default number of iterations to simulate.
default_nsteps_per_iteration: 500 # Number of timesteps per iteration.
default_timestep: 2.0 * femtosecond # Timestep for Langevin dyanmics.
replica_mixing_scheme: swap-all # Specify how to mix replicas. Possible values are
# swap-neighbors and swap-all.
constraint_tolerance: 1.0e-6 # Relative constraint tolerance.
# ALCHEMY PARAMETERS
# ------------------
annihilate_electrostatics: yes # If set, electrostatics is annihilated, rather than decoupled.
annihilate_sterics: no # If set, sterics (Lennard-Jones or Halgren potential) is annihilated,
# rather than decoupled.
softcore_alpha: 0.5 # Alchemical softcore parameter for Lennard-Jones.
softcore_beta: 0.0 # Alchemical softcore parameter for electrostatics.
# to recover standard electrostatic scaling.
softcore_a: 1 # Parameters modifying softcore Lennard-Jones form.
softcore_b: 1
softcore_c: 6
softcore_d: 1
softcore_e: 1
softcore_f: 2