SimulationSettings

pydantic model openfe.protocols.settings.SimulationSettings

Settings for simulation control, including lengths, writing to disk, etc…

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 minimization_steps = 5000

Number of minimization steps to perform. Default 5000.

field equilibration_length: Quantity [Required]

Length of the equilibration phase in units of time. The total number of steps from this equilibration length (i.e. equilibration_length / IntegratorSettings.timestep) must be a multiple of the value defined for IntegratorSettings.n_steps.

field production_length: Quantity [Required]

Length of the production phase in units of time. The total number of steps from this production length (i.e. production_length / IntegratorSettings.timestep) must be a multiple of the value defined for IntegratorSettings.nsteps.

field output_filename = 'simulation.nc'

Path to the trajectory storage file. Default ‘simulation.nc’.

field output_structure = 'hybrid_system.pdb'

Path of the output hybrid topology structure file. This is used to visualise and further manipulate the system. Default ‘hybrid_system.pdb’.

field output_indices = 'not water'

Selection string for which part of the system to write coordinates for. Default ‘not water’.

field checkpoint_interval = <Quantity(250, 'timestep')>

Frequency to write the checkpoint file. Default 250 * unit.timestep.

field checkpoint_storage = 'checkpoint.nc'

Separate filename for the checkpoint file. Note, this should not be a full path, just a filename. Default ‘checkpoint.nc’.

field forcefield_cache: str | None = 'db.json'

Filename for caching small molecule residue templates so they can be later reused.