openmmtools.mcmc.SequenceMove

class openmmtools.mcmc.SequenceMove(move_list, **kwargs)

A sequence of MCMC moves.

Parameters:

move_listlist-like of MCMCMove

The sequence of MCMC moves to apply.

Examples

NPT ensemble simulation of a Lennard Jones fluid with a sequence of moves.

>>> import numpy as np
>>> from openmm import unit
>>> from openmmtools import testsystems
>>> from openmmtools.states import ThermodynamicState, SamplerState
>>> test = testsystems.LennardJonesFluid(nparticles=200)
>>> thermodynamic_state = ThermodynamicState(system=test.system, temperature=298*unit.kelvin,
...                                          pressure=1*unit.atmospheres)
>>> sampler_state = SamplerState(positions=test.positions)
>>> # Create a move set that includes a Monte Carlo barostat move.
>>> move = SequenceMove([GHMCMove(n_steps=50), MonteCarloBarostatMove(n_attempts=5)])
>>> # Create an MCMC sampler instance and run 5 iterations of the simulation.
>>> sampler = MCMCSampler(thermodynamic_state, sampler_state, move=move)
>>> sampler.run(n_iterations=2)
>>> np.allclose(sampler.sampler_state.positions, test.positions)
False

Attributes:

move_listlist of MCMCMove

The sequence of MCMC moves to apply.

Methods

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

Apply the sequence of MCMC move in order.

__init__(move_list, **kwargs)

Methods

__init__(move_list, **kwargs)
apply(thermodynamic_state, sampler_state[, ...])	Apply the sequence of MCMC move in order.

Attributes

context_cache
statistics	The statistics of all moves as a list of dictionaries.