MCMC Moves Header for YAML Files

In the mcmc_moves section, you can define the propagators used to move forward the replicas of a sampler. This block is optional. By default, YANK uses a sequence of MCMC moves that mix MC rigid rotation and translation of the ligand with Langevin dynamics.

MCMC Moves Syntax

MCMC moves definitions must adhere to the following syntax

mcmc_moves:
    {UserDefinedMCMCMoveName1}:
        type: {MCMCMove}
        {MCMCMoveOptions}
    {UserDefinedMCMCMoveName2}:
        type: {MCMCMOve}
        {MCMCMoveOptions}
    ...

where {UserDefinedMCMCMoveName} is a unique string identifier within the mcmc_moves block. The only mandatory keyword is type. YANK supports all the MCMCMove classes defined in the openmmtools.mcmc module, which currently are:

  • SequenceMove: Container MCMC move describing a sequence of other moves.
  • LangevinSplittingDynamicsMove: High-quality Langevin integrator family based on symmetric Strang splittings, using g-BAOAB [27] as default
  • LangevinDynamicsMove: Leapfrog Langevin dynamics integrator from OpenMM (simtk.openmm.LangevinIntegrator); not recommended
  • GHMCMove: Metropolized Langevin integrator, when exact sampling is required; not recommended for large systems
  • HMCMove: Hybrid Monte Carlo integrator, when exact sampling is required; not recommended for large systems
  • MonteCarloBarostatMove: Explicit Monte Carlo barostat; not recommended, since this can be incorporated within Langevin dynamics moves instead
  • MCDisplacementMove: Monte Carlo displacement of ligand; useful for fragment-sized ligands in implicit solvent
  • MCRotationMove: Monte Carlo rotation of ligand; useful for fragment-sized ligands in implicit solvent

Each move accepts a specific set of options (see the constructor documentation of the classes in the openmmtools.mcmc module. The default moves used by YANK are equivalent to the following:

mcmc_moves:
    default1:
        type: LangevinSplittingDynamicsMove
        timestep: 2.0*femtoseconds # 2 fs timestep
        collision_rate: 1.0 / picosecond # weak collision rate
        n_steps: 500 # 500 steps/iteration
        reassign_velocities: yes # reassign Maxwell-Boltzmann velocities each iteration
        n_restart_attempts: 6 # attempt to recover from NaNs
        splitting: 'V R O R V' # use the high-quality BAOAB integrator
    default2:
        type: SequenceMove
        move_list:
            - type: MCDisplacementMove # Monte Carlo ligand displacement
            - type: MCRotationMove # Monte Carlo ligand rotation
            - type: LangevinSplittingDynamicsMove
              timestep: 2.0*femtoseconds # 2 fs timestep
              collision_rate: 1.0 / picosecond # weak collision rate
              n_steps: 500 # 500 steps/iteration
              reassign_velocities: yes # reassign Maxwell-Boltzmann velocities each iteration
              n_restart_attempts: 6 # attempt to recover from NaNs
              splitting: 'V R O R V' # use the high-quality BAOAB integrator

default1 is used for the solvent phase and for complex phases using a BoreschLike restraint. For complex phases using any other restraint, default2 is used.

Each iteration of the sampler applies the MCMC move once. In default2 example above, one iteration of the algorithm consists of one MC ligand rigid translation, followed by one MC ligand rigid rotation, and 500 steps of Langevin dynamics.