OpenMMSystemGeneratorFFSettings — gufe documentation

class gufe.settings.models.OpenMMSystemGeneratorFFSettings(*args: Any, **kwargs: Any)#

Parameters to set up the force field with OpenMM ForceFields

Note

Right now we just basically just grab what we need for the openmmforcefields.system_generators.SystemGenerator signature. See the OpenMMForceField SystemGenerator documentation for more details.

Methods

`allowed_nonbonded`
`constraint_check`
`is_positive_distance`

Attributes

`constraints`	Constraints to be applied to system.
`forcefields`	List of force field paths for all components except `SmallMoleculeComponent`
`hydrogen_mass`	Mass to be repartitioned to hydrogens from neighbouring heavy atoms (in amu), default 3.0
`nonbonded_cutoff`	Cutoff value for short range nonbonded interactions.
`nonbonded_method`	Method for treating nonbonded interactions, currently only PME and NoCutoff are allowed.
`rigid_water`	Whether to use a rigid water model.
`small_molecule_forcefield`	Name of the force field to be used for `SmallMoleculeComponent`

class Config#

Noindex:

classmethod allowed_nonbonded(v)#

classmethod constraint_check(v)#

constraints: str | None = 'hbonds'#: Constraints to be applied to system. One of ‘hbonds’, ‘allbonds’, ‘hangles’ or None, default ‘hbonds’

forcefields: list[str] = ['amber/ff14SB.xml', 'amber/tip3p_standard.xml', 'amber/tip3p_HFE_multivalent.xml', 'amber/phosaa10.xml']#: List of force field paths for all components except SmallMoleculeComponent

frozen_copy()#

A copy of this Settings object which cannot be modified

This is intended to be used by Protocols to make their stored Settings read-only

hydrogen_mass: float = 3.0#: Mass to be repartitioned to hydrogens from neighbouring heavy atoms (in amu), default 3.0

property is_frozen#: If this Settings object is frozen and cannot be modified

classmethod is_positive_distance(v)#

nonbonded_cutoff: openff.models.types.FloatQuantity.nanometer = <Quantity(1.0, 'nanometer')>#: Cutoff value for short range nonbonded interactions. Default 1.0 * unit.nanometer.

nonbonded_method = 'PME'#: Method for treating nonbonded interactions, currently only PME and NoCutoff are allowed. Default PME.

rigid_water: bool = True#: Whether to use a rigid water model. Default True

small_molecule_forcefield: str = 'openff-2.1.1'#: Name of the force field to be used for SmallMoleculeComponent

unfrozen_copy()#

A copy of this Settings object, which can be modified

Settings objects become frozen when within a Protocol. If you really need to reverse this, this method is how.

OpenMMSystemGeneratorFFSettings#

`OpenMMSystemGeneratorFFSettings`#