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