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