openmmtools.mcmc.MCDisplacementMove¶

class openmmtools.mcmc.MCDisplacementMove(displacement_sigma=Quantity(value=1.0, unit=nanometer), **kwargs)[source]¶

A metropolized move that randomly displace a subset of atoms.

Parameters:

displacement_sigma : simtk.unit.Quantity: The standard deviation of the normal distribution used to propose the random displacement (units of length, default is 1.0*nanometer).
atom_subset : slice or list of int, optional: If specified, the move is applied only to those atoms specified by these indices. If None, the move is applied to all atoms (default is None).
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).

See also

Attributes:	n_accepted : int The number of proposals accepted. n_proposed : int The total number of attempted moves. displacement_sigma atom_subset context_cache

Methods

`apply`(thermodynamic_state, sampler_state)	Apply a metropolized move to the sampler state.
`displace_positions`(positions[, …])	Return the positions after applying a random displacement to them.

__init__(displacement_sigma=Quantity(value=1.0, unit=nanometer), **kwargs)[source]¶: x.__init__(…) initializes x; see help(type(x)) for signature

Methods

`__init__`([displacement_sigma, unit])	x.__init__(…) initializes x; see help(type(x)) for signature
`apply`(thermodynamic_state, sampler_state)	Apply a metropolized move to the sampler state.
`displace_positions`(positions[, …])	Return the positions after applying a random displacement to them.

Attributes

statistics The acceptance statistics as a dictionary.

apply(thermodynamic_state, sampler_state)¶

Apply a metropolized move to the sampler state.

Total number of acceptances and proposed move are updated.

Parameters:	thermodynamic_state : openmmtools.states.ThermodynamicState The thermodynamic state to use to apply the move. sampler_state : openmmtools.states.SamplerState The initial sampler state to apply the move to. This is modified.

static displace_positions(positions, displacement_sigma=Quantity(value=1.0, unit=nanometer))[source]¶

Return the positions after applying a random displacement to them.

Parameters:	positions : nx3 numpy.ndarray simtk.unit.Quantity The positions to displace. displacement_sigma : simtk.unit.Quantity The standard deviation of the normal distribution used to propose the random displacement (units of length, default is 1.0*nanometer).
Returns:	rotated_positions : nx3 numpy.ndarray simtk.unit.Quantity The displaced positions.

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