openmmtools.mcmc.MonteCarloBarostatMove

class openmmtools.mcmc.MonteCarloBarostatMove(n_attempts=5, **kwargs)[source]

Monte Carlo barostat move.

This move makes one or more attempts to update the box volume using Monte Carlo updates.

Parameters:
n_attemptsint, optional

The number of Monte Carlo attempts to make to adjust the box volume (default is 5).

Examples

The thermodynamic state must be barostated by a MonteCarloBarostat force. The class ThermodynamicState takes care of adding one when we specify the pressure in its constructor.

>>> from openmm import unit
>>> from openmmtools import testsystems
>>> from openmmtools.states import ThermodynamicState, SamplerState
>>> test = testsystems.AlanineDipeptideExplicit()
>>> sampler_state = SamplerState(positions=test.positions)
>>> thermodynamic_state = ThermodynamicState(system=test.system, temperature=298*unit.kelvin,
...                                          pressure=1.0*unit.atmosphere)

Create a MonteCarloBarostatMove move with default parameters.

>>> move = MonteCarloBarostatMove()

or create a GHMC move with specified parameters.

>>> move = MonteCarloBarostatMove(n_attempts=2)

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
Attributes:
n_attempts

The number of MC attempts to make to adjust the box volume.

Methods

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

Apply the MCMC move.
__init__(n_attempts=5, **kwargs)[source]

Methods

__init__([n_attempts])

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

Apply the MCMC move.

Attributes

context_cache

n_attempts

The number of MC attempts to make to adjust the box volume.