AmoebaGeneralizedKirkwoodForce

class OpenMM::AmoebaGeneralizedKirkwoodForce : public OpenMM::Force

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().

Public Functions

inline 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

inline double getSolventDielectric() const

Get the dielectric constant for the solvent.

inline void setSolventDielectric(double dielectric)

Set the dielectric constant for the solvent.

inline double getSoluteDielectric() const

Get the dielectric constant for the solute.

inline 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.

inline virtual bool usesPeriodicBoundaryConditions() const

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

Returns

true if nonbondedMethod uses PBC and false otherwise