batter.config.run.FESimArgs#

pydantic model batter.config.run.FESimArgs[source]#

Free-energy simulation knobs loaded from the fe_sim section.

The fields feed directly into batter.config.simulation.SimulationConfig overrides. fe_type is resolved internally from protocol rather than being set by users.

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.

Config:

  • extra: str = forbid

Fields:
Validators:
field analysis_start_step: int = 0#

Only analyze FE production steps after this step (per window).

Constraints:

  • ge = 0

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

field barostat: int = 2#

Barostat selection (1=Berendsen, 2=MC).

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

field blocks: int = 0#

Number of MBAR blocks to use during analysis.

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

field buffer_x: float = 20.0#

Box padding along X (Å).

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

field buffer_y: float = 20.0#

Box padding along Y (Å).

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

field buffer_z: float = 20.0#

Box padding along Z (Å).

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

field component_lambdas: Dict[str, List[float]] [Optional]#

Per-component lambda overrides (key = letter).

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

field cut: float = 9.0#

Nonbonded cutoff (Å).

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

field dec_int: str = 'mbar'#

Free-energy integration scheme (mbar or ti).

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

field dt: float = 0.004#

MD timestep (ps).

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

field enable_mcwat: Literal['yes', 'no'] = 'yes'#

Enable MC water exchange moves during equilibration (1 = on).

Validated by:

  • _coerce_fe_yes_no

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

field eq_steps: int = 1000000#

Total equilibration steps (entire equilibration run).

Constraints:

  • ge = 0

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

field gamma_ln: float = 1.0#

Langevin gamma value (ps^-1).

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

field hmr: Literal['yes', 'no'] = 'no'#

Hydrogen mass repartitioning toggle.

Validated by:

  • _coerce_fe_yes_no

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

field lambdas: List[float] [Optional]#

Default lambda schedule when component-specific overrides are not provided.

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

  • _validate_lambdas

field lig_angle_force: float = 250.0#

Ligand angle restraint spring constant (kcal/mol/rad^2).

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

  • _validate_force_const

field lig_buffer: float = 15.0#

Ligand-specific box buffer (Å) for solvation boxes.

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

field lig_com_force: float = 10.0#

Ligand COM restraint spring constant (kcal/mol/Å^2).

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

  • _validate_force_const

field lig_dihcf_force: float = 0.0#

Ligand dihedral restraint spring constant (kcal/mol/rad^2).

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

field lig_distance_force: float = 5.0#

Ligand COM distance restraint spring constant (kcal/mol/Å^2).

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

  • _validate_force_const

field n_bootstraps: int = 0#

Number of MBAR bootstrap resamples used during FE analysis.

Constraints:

  • ge = 0

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

field n_steps: Dict[str, int] [Optional]#

Total production steps per component (key = letter).

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

field ntpr: int = 100#

Energy print frequency.

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

field ntwe: int = 0#

Energy write frequency (0 disables).

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

field ntwr: int = 2500#

Restart write frequency.

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

field ntwx: int = 25000#

Trajectory write frequency.

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

field rec_com_force: float = 10.0#

Protein COM restraint spring constant (kcal/mol/Å^2).

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

  • _validate_force_const

field remd: RemdArgs [Optional]#

Replica-exchange MD controls (nstlim).

Validated by:

  • _coerce_remd

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

field rocklin_correction: Literal['yes', 'no'] = 'no'#

Apply Rocklin correction during analysis.

Validated by:

  • _coerce_fe_yes_no

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

field temperature: float = 298.15#

Simulation temperature (K).

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs

field unbound_threshold: float = 8.0#

Distance threshold (Å) used to flag ligands as unbound during equilibration analysis.

Constraints:

  • ge = 0.0

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _reject_legacy_knobs