OpenMM Molecular Dynamics (MD) Protocol

A Protocol for running MD simulation using OpenMM.

Protocol API Specification

PlainMDProtocol	Protocol for running Molecular Dynamics simulations using OpenMM.
PlainMDSetupUnit	Protocol setup unit for plain MD simulations which handles charging, system building and solvation.
PlainMDSimulationUnit	Protocol unit for plain MD simulation equilibration and production runs (NonTransformation).
PlainMDProtocolResult	Dict-like container for the output of a PlainMDProtocol.

Protocol Settings

pydantic model openfe.protocols.openmm_md.plain_md_settings.PlainMDProtocolSettings

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]

Number of independent MD runs to perform.

field forcefield_settings: OpenMMSystemGeneratorFFSettings [Required]

field partial_charge_settings: OpenFFPartialChargeSettings [Required]

field solvation_settings: OpenMMSolvationSettings [Required]

field engine_settings: OpenMMEngineSettings [Required]

field integrator_settings: IntegratorSettings [Required]

field simulation_settings: MDSimulationSettings [Required]

field output_settings: MDOutputSettings [Required]

field thermo_settings: InstanceOf[ThermoSettings] [Required]