openmmtools.mcmc.BaseIntegratorMove

class openmmtools.mcmc.BaseIntegratorMove(n_steps, context_cache=None, reassign_velocities=False, n_restart_attempts=4)

A general MCMC move that applies an integrator.

This class is intended to be inherited by MCMCMoves that need to integrate the system. The child class has to implement the _get_integrator method.

You can decide to override _before_integration() and _after_integration() to execute some code at specific points of the workflow, for example to read data from the Context before the it is destroyed.

Parameters:

n_steps : int

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

context_cache : openmmtools.cache.ContextCache, optional

The ContextCache to use for Context creation. If None, the global cache openmmtools.cache.global_context_cache is used (default is None).

reassign_velocities : bool, optional

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

restart_attempts : int, optional

When greater than 0, if after the integration there are NaNs in energies, the move will restart. When the integrator has a random component, this may help recovering. On the last attempt, the Context is re-initialized in a slower process, but better than the simulation crashing. An IntegratorMoveError is raised after the given number of attempts if there are still NaNs.

Examples

Create a VerletIntegratorMove class.

>>> from openmmtools import testsystems, states
>>> from simtk.openmm import VerletIntegrator
>>> class VerletMove(BaseIntegratorMove):
...     def __init__(self, timestep, n_steps, **kwargs):
...         super(VerletMove, self).__init__(n_steps, **kwargs)
...         self.timestep = timestep
...     def _get_integrator(self, thermodynamic_state):
...         return VerletIntegrator(self.timestep)
...     def _before_integration(self, context, thermodynamic_state):
...         print('Setting velocities')
...         context.setVelocitiesToTemperature(thermodynamic_state.temperature)
...     def _after_integration(self, context, thermodynamic_state):
...         print('Reading statistics')
...
>>> alanine = testsystems.AlanineDipeptideVacuum()
>>> sampler_state = states.SamplerState(alanine.positions)
>>> thermodynamic_state = states.ThermodynamicState(alanine.system, 300*unit.kelvin)
>>> move = VerletMove(timestep=1.0*unit.femtosecond, n_steps=2)
>>> move.apply(thermodynamic_state, sampler_state)
Setting velocities
Reading statistics

Attributes:

n_steps : int

context_cache : openmmtools.cache.ContextCache

reassign_velocities : bool

restart_attempts : int or None

Methods

apply(thermodynamic_state, sampler_state)

Propagate the state through the integrator.

__init__(n_steps, context_cache=None, reassign_velocities=False, n_restart_attempts=4)

x.__init__(…) initializes x; see help(type(x)) for signature

Methods

__init__(n_steps[, context_cache, …])	x.__init__(…) initializes x; see help(type(x)) for signature
apply(thermodynamic_state, sampler_state)	Propagate the state through the integrator.

apply(thermodynamic_state, sampler_state)

Propagate the state through the integrator.

This updates the SamplerState after the integration. It also logs benchmarking information through the utils.Timer class.

Parameters:

thermodynamic_state : openmmtools.states.ThermodynamicState

The thermodynamic state to use to propagate dynamics.

sampler_state : openmmtools.states.SamplerState

The sampler state to apply the move to. This is modified.

See also

openmmtools.utils.Timer