HybridTopProtocolSettings#

pydantic model pontibus.protocols.relative.HybridTopProtocolSettings#

Configuration object for HybridTopologyRFEProtocol.

See also

pontibus.protocols.relative.HybridTopologyRFEProtocol

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

Config:

  • validate_assignment: bool = True

  • arbitrary_types_allowed: bool = True

  • extra: str = forbid

  • validate_default: bool = True

Fields:
Validators:
field forcefield_settings: InterchangeFFSettings [Required]#

Parameters to set up in the force field

frozen_copy()#

A copy of this Settings object which cannot be modified

This is intended to be used by Protocols to make their stored Settings read-only

classmethod get_defaults()#
property is_frozen#

If this Settings object is frozen and cannot be modified

validator must_be_positive  »  protocol_repeats#
unfrozen_copy()#

A copy of this Settings object, which can be modified

Settings objects become frozen when within a Protocol. If you really need to reverse this, this method is how.

field protocol_repeats: int [Required]#

The number of completely independent repeats of the entire sampling process. The mean of the repeats defines the final estimate of FE difference, while the variance between repeats is used as the uncertainty.

Validated by:

  • must_be_positive

field thermo_settings: ThermoSettings [Required]#

Settings for thermodynamic parameters.

field partial_charge_settings: OpenFFPartialChargeSettings [Required]#

Settings for assigning partial charges to small molecules.

field lambda_settings: LambdaSettings [Required]#

Lambda protocol settings including lambda windows and lambda functions.

field alchemical_settings: AlchemicalSettings [Required]#

Alchemical protocol settings including soft core scaling.

field simulation_settings: MultiStateSimulationSettings [Required]#

Settings for alchemical sampler.

field engine_settings: OpenMMEngineSettings [Required]#

Settings specific to the OpenMM engine such as the compute platform.

field integrator_settings: IntegratorSettings [Required]#

Settings for the integrator such as timestep and barostat settings.

field output_settings: MultiStateOutputSettings [Required]#

Simulation output control settings.

field solvation_settings: PackmolSolvationSettings | InterchangeOpenMMSolvationSettings [Required]#

Settings for solvating the system.