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_fe_range: Tuple[int, int] | None = None#

Optional (start, end) simulation index range to analyze per FE window.

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _ingest_remd_enable

  • _validate_analysis_range

field barostat: int = 2#

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

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _ingest_remd_enable

field blocks: int = 0#

Number of MBAR blocks to use during analysis.

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _ingest_remd_enable

field buffer_x: float = 20.0#

Box padding along X (Å).

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _ingest_remd_enable

field buffer_y: float = 20.0#

Box padding along Y (Å).

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _ingest_remd_enable

field buffer_z: float = 20.0#

Box padding along Z (Å).

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _ingest_remd_enable

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

Per-component lambda overrides (key = letter).

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _ingest_remd_enable

field cut: float = 9.0#

Nonbonded cutoff (Å).

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _ingest_remd_enable

field dec_int: str = 'mbar'#

Free-energy integration scheme (mbar or ti).

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _ingest_remd_enable

field dt: float = 0.004#

MD timestep (ps).

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _ingest_remd_enable

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

  • _ingest_remd_enable

field eq_steps: int = 1000000#

Steps per equilibration segment (applied to the initial run and each extend).

Constraints:

  • gt = 0

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _ingest_remd_enable

field gamma_ln: float = 1.0#

Langevin gamma value (ps^-1).

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _ingest_remd_enable

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

Hydrogen mass repartitioning toggle.

Validated by:

  • _coerce_fe_yes_no

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _ingest_remd_enable

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

  • _ingest_remd_enable

  • _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

  • _ingest_remd_enable

  • _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

  • _ingest_remd_enable

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

  • _ingest_remd_enable

  • _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

  • _ingest_remd_enable

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

  • _ingest_remd_enable

  • _validate_force_const

field ntpr: int = 1000#

Energy print frequency.

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _ingest_remd_enable

field ntwe: int = 0#

Energy write frequency (0 disables).

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _ingest_remd_enable

field ntwr: int = 2500#

Restart write frequency.

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _ingest_remd_enable

field ntwx: int = 25000#

Trajectory write frequency.

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _ingest_remd_enable

field num_equil_extends: int = 6#

Number of additional equilibration segments (all run fully released).

Constraints:

  • ge = 0

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _ingest_remd_enable

field num_fe_extends: int = 10#

# restarts per λ (controls how many FE simulations run per window).

Constraints:

  • ge = 1

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _ingest_remd_enable

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

  • _ingest_remd_enable

  • _validate_force_const

field remd: RemdArgs [Optional]#

Replica-exchange MD controls (nstlim/numexchg).

Validated by:

  • _coerce_remd

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _ingest_remd_enable

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

Toggle REMD execution (yes/no).

Validated by:

  • _coerce_remd_enable

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _ingest_remd_enable

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

  • _ingest_remd_enable

field steps1: Dict[str, int] [Optional]#

Stage 1 steps per component (key = letter).

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _ingest_remd_enable

field steps2: Dict[str, int] [Optional]#

Stage 2 steps per component (key = letter).

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _ingest_remd_enable

field temperature: float = 298.15#

Simulation temperature (K).

Validated by:

  • _ingest_component_lambda_fields

  • _ingest_legacy_step_fields

  • _ingest_remd_enable

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

  • _ingest_remd_enable