OpenMM Absolute Binding Free Energy Protocol#

This section provides details about the OpenMM Absolute Binding Free Energy Protocol implemented in OpenFE.

Protocol API specification#

AbsoluteBindingProtocol

Absolute binding free energy calculations using OpenMM and OpenMMTools.

AbsoluteBindingComplexUnit

Protocol Unit for the complex phase of an absolute binding free energy

AbsoluteBindingSolventUnit

Protocol Unit for the solvent phase of an absolute binding free energy

AbsoluteBindingProtocolResult

Dict-like container for the output of a AbsoluteBindingProtocol

Protocol Settings#

Below are the settings which can be tweaked in the protocol. The default settings (accessed using AbsoluteBindingProtocol.default_settings()) will automatically populate settings which we have found to be useful for running binding free energy calculations. There will however be some cases (such as when calculating difficult to converge systems) where you will need to tweak some of the following settings.

pydantic model openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteBindingSettings#

Configuration object for AbsoluteBindingPProtocol

See also

openfe.protocols.openmm_afe.AbsoluteBindingProtocol

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 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 forcefield_settings: OpenMMSystemGeneratorFFSettings [Required]#

Parameters to set up the force field with OpenMM Force Fields

field thermo_settings: ThermoSettings [Required]#

Settings for thermodynamic parameters

field solvent_solvation_settings: OpenMMSolvationSettings [Required]#

Settings for solvating the system in the solvent.

field complex_solvation_settings: OpenMMSolvationSettings [Required]#

Settings for solvating the system in the complex.

field alchemical_settings: AlchemicalSettings [Required]#

Alchemical protocol settings.

field complex_lambda_settings: LambdaSettings [Required]#

Settings for controlling the complex transformation leg lambda schedule for the different components (vdw, elec, restraints).

field solvent_lambda_settings: LambdaSettings [Required]#

Settings for controlling the solvent transformation leg lambda schedule for the different components (vdw, elec, restraints).

Notes

  • The restraints entry of the lambda settings will be ignored in the solvent leg.

field engine_settings: OpenMMEngineSettings [Required]#

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

field integrator_settings: IntegratorSettings [Required]#

Settings for controlling the integrator, such as the timestep and barostat settings.

field complex_equil_simulation_settings: MDSimulationSettings [Required]#

Pre-alchemical complex simulation control settings.

field complex_simulation_settings: MultiStateSimulationSettings [Required]#

Simulation control settings, including simulation lengths for the complex 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 complex_equil_output_settings: ABFEPreEquilOutputSettings [Required]#

Simulation output settings for the complex non-alchemical equilibration.

field complex_output_settings: MultiStateOutputSettings [Required]#

Simulation output settings for the complex transformation.

field solvent_equil_output_settings: ABFEPreEquilOutputSettings [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 restraint_settings: BaseRestraintSettings [Required]#

Settings controlling how restraints are added to the system in the complex simulation.