Absolute Solvation Free Energy (ASFE) Protocol#

A Protocol for running solvation free energy calculations with any arbitrary single composition solvent.

Protocol API Specification#

`ASFEProtocol`
`ASFEProtocolResult`	Results class for the ASFEProtocol.
`ASFESettings`	Configuration object for `ASFEProtocol`.
`ASFESolventUnit`	Protocol Unit for the solvent phase of an absolute solvation free energy
`ASFEVacuumUnit`	Protocol Unit for the vacuum phase of an absolute solvation free energy

pydantic model pontibus.protocols.solvation.settings.ASFESettings#

Configuration object for ASFEProtocol.

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 solvent_forcefield_settings: InterchangeFFSettings [Required]#: Parameters to set up in the solvent 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 alchemical_settings: AlchemicalSettings [Required]#: Alchemical protocol settings.

field lambda_settings: LambdaSettings [Required]#: Settings for controlling the lambda schedule for the different components (vdw, elec, restraints).

field vacuum_engine_settings: OpenMMEngineSettings [Required]#: Settings specific to the OpenMM engine, such as the compute platform for the vacuum transformation.

field solvent_engine_settings: OpenMMEngineSettings [Required]#: Settings specific to the OpenMM engine, such as the compute platform for the solvent transformation.

field integrator_settings: IntegratorSettings [Required]#: Settings for controlling the integrator, such as the timestep and barostat settings.

field vacuum_equil_simulation_settings: MDSimulationSettings [Required]#

Pre-alchemical vacuum simulation control settings.

Notes

The NVT equilibration should be set to 0 * unit.nanosecond as it will not be run.

field vacuum_simulation_settings: MultiStateSimulationSettings [Required]#: Simulation control settings, including simulation lengths for the vacuum transformation.

field solvent_equil_simulation_settings: MDSimulationSettings [Required]#: Pre-alchemical solvent simulation control settings.

field solvent_simulation_settings: MultiStateSimulationSettings [Required]#: Simulation control settings, including simulation lengths for the solvent transformation.

field vacuum_equil_output_settings: MDOutputSettings [Required]#: Simulation output settings for the vacuum non-alchemical equilibration.

field vacuum_output_settings: MultiStateOutputSettings [Required]#: Simulation output settings for the vacuum transformation.

field solvent_equil_output_settings: MDOutputSettings [Required]#: Simulation output settings for the solvent non-alchemical equilibration.

field solvent_output_settings: MultiStateOutputSettings [Required]#: Simulation output settings for the solvent transformation.

field partial_charge_settings: OpenFFPartialChargeSettings [Required]#: Settings for controlling how to assign partial charges, including the partial charge assignment method, and the number of conformers used to generate the partial charges.

field vacuum_forcefield_settings: InterchangeFFSettings [Required]#: Parameters to set up the vacuum force field

field solvation_settings: PackmolSolvationSettings [Required]#: Settings for solvating the system.