AmoebaGeneralizedKirkwoodForce

class simtk.openmm.openmm.AmoebaGeneralizedKirkwoodForce(*args)

This class implements an implicit solvation force using the generalized Kirkwood/Grycuk model.

To use this class, create an AmoebaGeneralizedKirkwoodForce object, then call addParticle() once for each particle in the System to define its parameters. The number of particles for which you define parameters must be equal to the number of particles in the System, or else an exception will be thrown when you try to create a Context. After a particle has been added, you can modify its force field parameters by calling setParticleParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

__init__(self) → AmoebaGeneralizedKirkwoodForce

__init__(self, other) -> AmoebaGeneralizedKirkwoodForce

This class implements an implicit solvation force using the generalized Kirkwood/Grycuk model.

To use this class, create an AmoebaGeneralizedKirkwoodForce object, then call addParticle() once for each particle in the System to define its parameters. The number of particles for which you define parameters must be equal to the number of particles in the System, or else an exception will be thrown when you try to create a Context. After a particle has been added, you can modify its force field parameters by calling setParticleParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

Methods

__init__(self) __init__(self, other) -> AmoebaGeneralizedKirkwoodForce
addParticle(self, charge, radius, scalingFactor) Add the parameters for a particle.
getForceGroup(self) Get the force group this Force belongs to.
getIncludeCavityTerm(self) Get the flag signaling whether the cavity term should be included
getNumParticles(self) Get the number of particles in the system.
getParticleParameters(self, index) Get the force field parameters for a particle.
getProbeRadius(self) Get the probe radius (nm) used in SASA contribution
getSoluteDielectric(self) Get the dielectric constant for the solute.
getSolventDielectric(self) Get the dielectric constant for the solvent.
getSurfaceAreaFactor(self) Get the surface area factor kJ/(nm*nm) used in SASA contribution
setForceGroup(self, group) Set the force group this Force belongs to.
setIncludeCavityTerm(self, includeCavityTerm) Set the flag signaling whether the cavity term should be included
setParticleParameters(self, index, charge, …) Set the force field parameters for a particle.
setProbeRadius(self, probeRadius) Set the probe radius (nm) used in SASA contribution
setSoluteDielectric(self, dielectric) Set the dielectric constant for the solute.
setSolventDielectric(self, dielectric) Set the dielectric constant for the solvent.
setSurfaceAreaFactor(self, surfaceAreaFactor) Set the surface area factor kJ/(nm*nm) used in SASA contribution
updateParametersInContext(self, context) Update the per-particle parameters in a Context to match those stored in this Force object.
usesPeriodicBoundaryConditions(self) Returns whether or not this force makes use of periodic boundary conditions.
getNumParticles(self) → int

Get the number of particles in the system.

addParticle(self, charge, radius, scalingFactor) → int

Add the parameters for a particle. This should be called once for each particle in the System. When it is called for the i’th time, it specifies the parameters for the i’th particle.

Parameters:
  • charge (double) – the charge of the particle, measured in units of the proton charge
  • radius (double) – the atomic radius of the particle, measured in nm
  • scalingFactor (double) – the scaling factor for the particle
Returns:

the index of the particle that was added
Return type:

int
getParticleParameters(self, index)

Get the force field parameters for a particle.

Parameters:index (int) – the index of the particle for which to get parameters
Returns:
  • charge (double) – the charge of the particle, measured in units of the proton charge
  • radius (double) – the atomic radius of the particle, measured in nm
  • scalingFactor (double) – the scaling factor for the particle
setParticleParameters(self, index, charge, radius, scalingFactor)

Set the force field parameters for a particle.

Parameters:
  • index (int) – the index of the particle for which to set parameters
  • charge (double) – the charge of the particle, measured in units of the proton charge
  • radius (double) – the atomic radius of the particle, measured in nm
  • scalingFactor (double) – the scaling factor for the particle
getSolventDielectric(self) → double

Get the dielectric constant for the solvent.

setSolventDielectric(self, dielectric)

Set the dielectric constant for the solvent.

getSoluteDielectric(self) → double

Get the dielectric constant for the solute.

setSoluteDielectric(self, dielectric)

Set the dielectric constant for the solute.

getIncludeCavityTerm(self) → int

Get the flag signaling whether the cavity term should be included

setIncludeCavityTerm(self, includeCavityTerm)

Set the flag signaling whether the cavity term should be included

getProbeRadius(self) → double

Get the probe radius (nm) used in SASA contribution

setProbeRadius(self, probeRadius)

Set the probe radius (nm) used in SASA contribution

getSurfaceAreaFactor(self) → double

Get the surface area factor kJ/(nm*nm) used in SASA contribution

setSurfaceAreaFactor(self, surfaceAreaFactor)

Set the surface area factor kJ/(nm*nm) used in SASA contribution

updateParametersInContext(self, context)

Update the per-particle parameters in a Context to match those stored in this Force object. This method provides an efficient method to update certain parameters in an existing Context without needing to reinitialize it. Simply call setParticleParameters() to modify this object’s parameters, then call updateParametersInContext() to copy them over to the Context.

The only information this method updates is the values of per-particle parameters. All other aspects of the Force (the probe radius, the surface area factor, etc.) are unaffected and can only be changed by reinitializing the Context.

usesPeriodicBoundaryConditions(self) → bool

Returns whether or not this force makes use of periodic boundary conditions.

Returns:true if nonbondedMethod uses PBC and false otherwise
Return type:bool
__copy__(self) → Force
getForceGroup(self) → int

Get the force group this Force belongs to.

setForceGroup(self, group)

Set the force group this Force belongs to.

Parameters:group (int) – the group index. Legal values are between 0 and 31 (inclusive).