openmmtools.mcmc.LangevinDynamicsMove

class openmmtools.mcmc.LangevinDynamicsMove(timestep=Quantity(value=1.0, unit=femtosecond), collision_rate=Quantity(value=10.0, unit=/picosecond), n_steps=1000, reassign_velocities=False, constraint_tolerance=1e-08, **kwargs)

Langevin dynamics segment as a (pseudo) Monte Carlo move.

This move assigns a velocity from the Maxwell-Boltzmann distribution and executes a number of Maxwell-Boltzmann steps to propagate dynamics. This is not a true Monte Carlo move, in that the generation of the correct distribution is only exact in the limit of infinitely small timestep; in other words, the discretization error is assumed to be negligible. Use HybridMonteCarloMove instead to ensure the exact distribution is generated.

The OpenMM LangevinMiddleIntegrator, based on BAOAB [1], is used.

Warning

The LangevinMiddleIntegrator generates velocities that are half a timestep lagged behind the positions.

Warning

No Metropolization is used to ensure the correct phase space distribution is sampled. This means that timestep-dependent errors will remain uncorrected, and are amplified with larger timesteps. Use this move at your own risk!

Parameters:

timestepopenmm.unit.Quantity, optional

The timestep to use for Langevin integration (time units, default is 1*openmm.unit.femtosecond).

collision_rateopenmm.unit.Quantity, optional

The collision rate with fictitious bath particles (1/time units, default is 10/openmm.unit.picoseconds).

n_stepsint, optional

The number of integration timesteps to take each time the move is applied (default is 1000).

reassign_velocitiesbool, optional

If True, the velocities will be reassigned from the Maxwell-Boltzmann distribution at the beginning of the move (default is False).

constraint_tolerancefloat, optional

Fraction of the constrained distance within which constraints are maintained for the integrator (default is 1e-8).

References

[1] Leimkuhler B and Matthews C. Robust and efficient configurational molecular sampling via Langevin dynamics. https://doi.org/10.1063/1.4802990 [2] Leimkuhler B and Matthews C. Efficient molecular dynamics using geodesic integration and solvent–solute splitting. https://doi.org/10.1098/rspa.2016.0138

Examples

First we need to create the thermodynamic state and the sampler state to propagate. Here we create an alanine dipeptide system in vacuum.

>>> from openmm import unit
>>> from openmmtools import testsystems
>>> from openmmtools.states import SamplerState, ThermodynamicState
>>> test = testsystems.AlanineDipeptideVacuum()
>>> sampler_state = SamplerState(positions=test.positions)
>>> thermodynamic_state = ThermodynamicState(system=test.system, temperature=298*unit.kelvin)

Create a Langevin move with default parameters

>>> move = LangevinDynamicsMove()

or create a Langevin move with specified parameters.

>>> move = LangevinDynamicsMove(timestep=0.5*unit.femtoseconds,
...                             collision_rate=20.0/unit.picoseconds, n_steps=10)

Perform one update of the sampler state. The sampler state is updated with the new state.

>>> move.apply(thermodynamic_state,sampler_state,context_cache=context_cache)
>>> np.allclose(sampler_state.positions, test.positions)
False

The same move can be applied to a different state, here an ideal gas.

>>> test = testsystems.IdealGas()
>>> sampler_state = SamplerState(positions=test.positions)
>>> thermodynamic_state = ThermodynamicState(system=test.system,
...                                          temperature=298*unit.kelvin)
>>> move.apply(thermodynamic_state,sampler_state,context_cache=context_cache)
>>> np.allclose(sampler_state.positions, test.positions)
False

Attributes:

timestepopenmm.unit.Quantity

The timestep to use for Langevin integration (time units).

collision_rateopenmm.unit.Quantity

The collision rate with fictitious bath particles (1/time units).

n_stepsint

The number of integration timesteps to take each time the move is applied.

reassign_velocitiesbool

If True, the velocities will be reassigned from the Maxwell-Boltzmann distribution at the beginning of the move.

constraint_tolerancefloat

Fraction of the constrained distance within which constraints are maintained for the integrator.

Methods

apply(thermodynamic_state, sampler_state[, ...])

Apply the Langevin dynamics MCMC move.

__init__(timestep=Quantity(value=1.0, unit=femtosecond), collision_rate=Quantity(value=10.0, unit=/picosecond), n_steps=1000, reassign_velocities=False, constraint_tolerance=1e-08, **kwargs)

Methods

__init__([timestep, collision_rate, ...])
apply(thermodynamic_state, sampler_state[, ...])	Apply the Langevin dynamics MCMC move.

Attributes

context_cache