GROMACS Molecular Dynamics (MD) Protocol

A Protocol for running MD simulation using GROMACS.

Protocol API Specification

GromacsMDProtocol	Protocol for running Molecular Dynamics simulations using Gromacs.
GromacsMDProtocolResult	Dict-like container for the output of a Gromacs MDProtocol.
GromacsMDProtocolSettings	Create a new model by parsing and validating input data from keyword arguments.
GromacsMDSetupUnit	Protocol unit for settings up plain MD simulations (NonTransformation).
GromacsMDRunUnit	Protocol unit for running plain MD simulations (NonTransformation) in Gromacs.

Protocol Settings

pydantic model openfe_gromacs.protocols.gromacs_md.md_settings.GromacsMDProtocolSettings

Create a new model by parsing and validating input data from keyword arguments.

Raises ValidationError if the input data cannot be parsed to form a valid model.

field thermo_settings: ThermoSettings [Required]

field protocol_repeats: int [Required]

Number of independent MD runs to perform.

field gro: str [Required]

field top: str [Required]

field forcefield_settings: FFSettingsOpenMM [Required]

field partial_charge_settings: OpenFFPartialChargeSettings [Required]

field solvation_settings: SolvationSettings [Required]

field integrator_settings: IntegratorSettings [Required]

field simulation_settings_em: EMSimulationSettings [Required]

field simulation_settings_nvt: NVTSimulationSettings [Required]

field simulation_settings_npt: NPTSimulationSettings [Required]

field engine_settings: GromacsEngineSettings [Required]

field output_settings_em: EMOutputSettings [Required]

field output_settings_nvt: NVTOutputSettings [Required]

field output_settings_npt: NPTOutputSettings [Required]