openmmtools.mcmc.LangevinSplittingDynamicsMove¶
- class openmmtools.mcmc.LangevinSplittingDynamicsMove(timestep=Quantity(value=1.0, unit=femtosecond), collision_rate=Quantity(value=10.0, unit=/picosecond), n_steps=1000, reassign_velocities=False, splitting='V R O R V', constraint_tolerance=1e-08, measure_shadow_work=False, measure_heat=False, **kwargs)[source]¶
Langevin dynamics segment with custom splitting of the operators and optional Metropolized Monte Carlo validation.
Besides all the normal properties of the
LangevinDynamicsMove
, this class implements the custom splitting sequence of theopenmmtools.integrators.LangevinIntegrator
. Additionally, the steps can be wrapped around a proper Generalized Hybrid Monte Carlo step to ensure that the exact distribution is generated.- 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).
- splittingstring, default: “V R O R V”
Sequence of “R”, “V”, “O” (and optionally “{”, “}”, “V0”, “V1”, …) substeps to be executed each timestep.
Forces are only used in V-step. Handle multiple force groups by appending the force group index to V-steps, e.g. “V0” will only use forces from force group 0. “V” will perform a step using all forces. “{” will cause metropolization, and must be followed later by a “}”.
- constraint_tolerancefloat, default: 1.0e-8
Tolerance for constraint solver
- measure_shadow_workboolean, default: False
Accumulate the shadow work performed by the symplectic substeps, in the global shadow_work
- measure_heatboolean, default: False
Accumulate the heat exchanged with the bath in each step, in the global heat
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 = LangevinSplittingDynamicsMove()
or create a Langevin move with specified splitting.
>>> move = LangevinSplittingDynamicsMove(splitting="O { V R V } O")
Where this splitting is a 5 step symplectic integrator:
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.
- splittingstr
Splitting applied to this integrator represented as a string.
- constraint_tolerancefloat, default: 1.0e-8
Tolerance for constraint solver
- measure_shadow_workboolean, default: False
Accumulate the shadow work performed by the symplectic substeps, in the global shadow_work
- measure_heatboolean, default: False
Accumulate the heat exchanged with the bath in each step, in the global heat
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, splitting='V R O R V', constraint_tolerance=1e-08, measure_shadow_work=False, measure_heat=False, **kwargs)[source]¶
Methods
__init__
([timestep, collision_rate, ...])apply
(thermodynamic_state, sampler_state[, ...])Apply the Langevin dynamics MCMC move.
Attributes
context_cache