AmoebaGeneralizedKirkwoodForce¶

class OpenMM::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

`AmoebaGeneralizedKirkwoodForce()`
`getNumParticles()`	Get the number of particles in the system.
`addParticle()`	Add the parameters for a particle.
`getParticleParameters()`	Get the force field parameters for a particle.
`setParticleParameters()`	Set the force field parameters for a particle.
`getSolventDielectric()`	Get the dielectric constant for the solvent.
`setSolventDielectric()`	Set the dielectric constant for the solvent.
`getSoluteDielectric()`	Get the dielectric constant for the solute.
`setSoluteDielectric()`	Set the dielectric constant for the solute.
`getIncludeCavityTerm()`	Get the flag signaling whether the cavity term should be included
`setIncludeCavityTerm()`	Set the flag signaling whether the cavity term should be included
`getProbeRadius()`	Get the probe radius (nm) used in SASA contribution
`setProbeRadius()`	Set the probe radius (nm) used in SASA contribution
`getSurfaceAreaFactor()`	Get the surface area factor kJ/(nm*nm) used in SASA contribution
`setSurfaceAreaFactor()`	Set the surface area factor kJ/(nm*nm) used in SASA contribution
`updateParametersInContext()`	Update the per-particle parameters in a `Context` to match those stored in this `Force` object.
`usesPeriodicBoundaryConditions()`	Returns whether or not this force makes use of periodic boundary conditions.

AmoebaGeneralizedKirkwoodForce()¶

int getNumParticles() const¶: Get the number of particles in the system.

int addParticle(double charge, double radius, double scalingFactor)¶

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 – the charge of the particle, measured in units of the proton charge
radius – the atomic radius of the particle, measured in nm
scalingFactor – the scaling factor for the particle

Returns:	the index of the particle that was added

void getParticleParameters(int index, double &charge, double &radius, double &scalingFactor) const¶

Get the force field parameters for a particle.

Parameters:

index – the index of the particle for which to get parameters
charge – [out] the charge of the particle, measured in units of the proton charge
radius – [out] the atomic radius of the particle, measured in nm
scalingFactor – [out] the scaling factor for the particle

void setParticleParameters(int index, double charge, double radius, double scalingFactor)¶

Set the force field parameters for a particle.

Parameters:

index – the index of the particle for which to set parameters
charge – the charge of the particle, measured in units of the proton charge
radius – the atomic radius of the particle, measured in nm
scalingFactor – the scaling factor for the particle

double getSolventDielectric() const¶: Get the dielectric constant for the solvent.

void setSolventDielectric(double dielectric)¶: Set the dielectric constant for the solvent.

double getSoluteDielectric() const¶: Get the dielectric constant for the solute.

void setSoluteDielectric(double dielectric)¶: Set the dielectric constant for the solute.

int getIncludeCavityTerm() const¶: Get the flag signaling whether the cavity term should be included

void setIncludeCavityTerm(int includeCavityTerm)¶: Set the flag signaling whether the cavity term should be included

double getProbeRadius() const¶: Get the probe radius (nm) used in SASA contribution

void setProbeRadius(double probeRadius)¶: Set the probe radius (nm) used in SASA contribution

double getSurfaceAreaFactor() const¶: Get the surface area factor kJ/(nm*nm) used in SASA contribution

void setSurfaceAreaFactor(double surfaceAreaFactor)¶: Set the surface area factor kJ/(nm*nm) used in SASA contribution

void updateParametersInContext(Context &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.

bool usesPeriodicBoundaryConditions() const¶

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

Returns:	true if nonbondedMethod uses PBC and false otherwise