batter.config.run.MDSimArgs#

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

Simulation overrides used when protocol == "md".

These runs reuse the equilibration steps from ABFE but never schedule FE windows, so only generic MD knobs are required (no lambdas, SDR restraints, etc.).

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:

  • _coerce_hmr » enable_mcwat

  • _coerce_hmr » hmr

  • _reject_legacy_knobs » all fields

field barostat: int = 2#

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

Validated by:

  • _reject_legacy_knobs

field cut: float = 9.0#

Nonbonded cutoff (Å).

Validated by:

  • _reject_legacy_knobs

field dt: float = 0.004#

MD timestep (ps).

Validated by:

  • _reject_legacy_knobs

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

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

Validated by:

  • _coerce_hmr

  • _reject_legacy_knobs

field eq_steps: int = 100000#

Total equilibration steps (entire equilibration run).

Constraints:

  • ge = 0

Validated by:

  • _reject_legacy_knobs

field gamma_ln: float = 1.0#

Langevin gamma value (ps^-1).

Validated by:

  • _reject_legacy_knobs

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

Hydrogen mass repartitioning toggle.

Validated by:

  • _coerce_hmr

  • _reject_legacy_knobs

field ntpr: int = 100#

Energy print frequency.

Validated by:

  • _reject_legacy_knobs

field ntwe: int = 0#

Energy write frequency (0 disables).

Validated by:

  • _reject_legacy_knobs

field ntwr: int = 10000#

Restart write frequency.

Validated by:

  • _reject_legacy_knobs

field ntwx: int = 25000#

Trajectory write frequency.

Validated by:

  • _reject_legacy_knobs

field temperature: float = 298.15#

Simulation temperature (K).

Validated by:

  • _reject_legacy_knobs