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.
PlainMDProtocolUnit	Protocol unit for plain MD simulations (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]