AmoebaGeneralizedKirkwoodForce

class 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.

This method is provided for backwards compatibility. Compared to the alternative five parameter addParticle method, the descreenRadius parameter is set to base radius value and the neckFactor is set to zero (no neck descreening).

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

int addParticle(double charge, double radius, double scalingFactor, double descreenRadius, double neckFactor)

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.

For generalized Born / generalized Kirkwood methods, the radius of each atom has two roles. The first is to define the base radius of the atom when computing its effective radius. This base radius is usually parameterized against solvation free energy differences. The second role is to describe how much continuum water is displaced when the atom descreens water for the calculation of the Born radii of other atoms. Separation of the two roles into the “radius” and “descreenRadius” parameters gives model developers more control over these separate roles.

For example, the fitting of base “radius” values will usually result in deviation from the force field’s van der Waals definition of Rmin (or sigma). The descreenRadius can be defined separately using force field van der Waals Rmin values, which maintains consistency of atomic sizes during the HCT pairwise descreening integral. The “scalingFactor” is applied to the descreenRadius during the HCT pairwise descreening integral, while the neckFactor (if greater than zero) includes neck contributions to descreening.

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 (unitless)

  • descreenRadius – the atomic radius of the particle for descreening, measure in nm

  • neckFactor – the scaling factor for interstitial neck descreening (unitless)

Returns

the index of the particle that was added

void getParticleParameters(int index, double &charge, double &radius, double &scalingFactor, double &descreenRadius, double &neckFactor) 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

  • descreenRadius – [out] the atomic radius of the particle for descreening, measure in nm

  • neckFactor – [out] the scaling factor for interstitial neck descreening (unitless)

void setParticleParameters(int index, double charge, double radius, double scalingFactor, double descreenRadius, double neckFactor)

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

  • descreenRadius – the atomic radius of the particle for descreening, measure in nm

  • neckFactor – the scaling factor for interstitial neck descreening (unitless)

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.

Parameters

dielectric – The solute dielectric constant.

inline bool getTanhRescaling() const

Get the flag signaling whether the solute descreening integral is rescaled by a Tanh function to account for interstitial spaces. If True then tanh rescaling is used.

inline void setTanhRescaling(bool tanhRescale)

Set the flag signaling whether the solute descreening integral is rescaled by a Tanh function to account for interstitial spaces.

Parameters

tanhRescale – False to turn off Tanh rescaling; true to turn on.

inline void getTanhParameters(double &b0, double &b1, double &b2) const

Get Tanh function parameters b0, b1 and b2.

Parameters

  • b0 – The first tanh parameter.

  • b1 – The second tanh parameter.

  • b2 – The third tanh parameter.

inline void setTanhParameters(double b0, double b1, double b2)

Set the the Tanh function parameters to account for interstitial spaces.

Parameters

  • b0 – The first tanh parameter.

  • b1 – The second tanh parameter.

  • b2 – The third tanh parameter.

double getDescreenOffset() const

Get the offset added to the atomic radius of each atom that sets the beginning of the descreening integral when calculating effective Born radii.

void setDescreenOffset(double descreenOffet)

Get the offset added to the atomic radius of each atom that sets the beginning of the descreening integral when calculating effective Born radii.

Parameters

descreenOffet – The descreening offset (nm).

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.

Parameters

includeCavityTerm – Zero to turn off the cavity term; one to turn on.

double getProbeRadius() const

Get the probe radius (nm) used for the cavity contribution.

void setProbeRadius(double probeRadius)

Set the probe radius (nm) used for the cavity contribution.

Parameters

probeRadius – The probeRadius for the cavity term.

double getDielectricOffset() const

Get the dielectric offset (nm) used for cavity contribution.

void setDielectricOffset(double dielectricOffset)

Set the dielectric offset (nm) used for cavity contribution.

Parameters

dielectricOffset – The dielectric offset (nm).

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.

Parameters

surfaceAreaFactor – The surface area factor in kJ/(nm*nm).

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