Hybrid Topology Relative Binding Free Energy (RBFE) Protocol#

An extension of the openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocol which purely uses OpenFF for system parameterization.

Protocol API Specification#

`HybridTopProtocol`	Relative Free Energy calculations using OpenMM and OpenMMTools.
`HybridTopProtocolResult`	Results class for the HybridTopologyProtocol class.
`HybridTopProtocolSettings`	Configuration object for `HybridTopologyRFEProtocol`.
`HybridTopProtocolSetupUnit`	Setup unit for the HybridTopProtocol.

pydantic model pontibus.protocols.relative.settings.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.

field forcefield_settings: InterchangeFFSettings [Required]#: Parameters to set up in the force field

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.

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.