This class implements an implicit solvation force using the GB/VI model. More...

#include <GBVIForce.h>

Inheritance diagram for GBVIForce:

Public Types
enum	NonbondedMethod { NoCutoff = 0, CutoffNonPeriodic = 1, CutoffPeriodic = 2 }
	This is an enumeration of the different methods that may be used for handling long range nonbonded forces. More...

enum	BornRadiusScalingMethod { NoScaling = 0, QuinticSpline = 1 }
	This is an enumeration of the different methods that may be used for scaling of the Born radii. More...

Public Member Functions
	GBVIForce ()

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

int	addParticle (double charge, double radius, double gamma)
	Add the GB/VI parameters for a particle.

void	getParticleParameters (int index, double &charge, double &radius, double &gamma) const
	Get the force field parameters for a particle.

void	setParticleParameters (int index, double charge, double radius, double gamma)
	Set the force field parameters for a particle.

int	addBond (int particle1, int particle2, double distance)
	Add a bond.

void	getBondParameters (int index, int &particle1, int &particle2, double &distance) const
	Get the parameters defining a bond.

void	setBondParameters (int index, int particle1, int particle2, double bondLength)
	Set 1-2 bonds.

int	getNumBonds (void) const
	Get number of bonds.

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.

NonbondedMethod	getNonbondedMethod () const
	Get the method used for handling long range nonbonded interactions.

void	setNonbondedMethod (NonbondedMethod method)
	Set the method used for handling long range nonbonded interactions.

double	getCutoffDistance () const
	Get the cutoff distance (in nm) being used for nonbonded interactions.

void	setCutoffDistance (double distance)
	Set the cutoff distance (in nm) being used for nonbonded interactions.

BornRadiusScalingMethod	getBornRadiusScalingMethod (void) const
	Get Born radius scaling method.

void	setBornRadiusScalingMethod (BornRadiusScalingMethod method)
	Set Born radius scaling method.

double	getQuinticLowerLimitFactor (void) const
	Get the lower limit factor used in the quintic spline scaling method (typically 0.5-0.8)

void	setQuinticLowerLimitFactor (double quinticLowerLimitFactor)
	Set the lower limit factor used in the quintic spline scaling method (typically 0.5-0.8)

double	getQuinticUpperBornRadiusLimit (void) const
	Get the upper limit used in the quintic spline scaling method, measured in nm (~5.0)

void	setQuinticUpperBornRadiusLimit (double quinticUpperBornRadiusLimit)
	Set the upper limit used in the quintic spline scaling method, measured in nm (~5.0)

Public Member Functions inherited from Force
	Force ()

virtual	~Force ()

int	getForceGroup () const
	Get the force group this Force belongs to.

void	setForceGroup (int group)
	Set the force group this Force belongs to.

Protected Member Functions
ForceImpl *	createImpl ()
	When a Context is created, it invokes this method on each Force in the System.

Protected Member Functions inherited from Force
ForceImpl &	getImplInContext (Context &context)
	Get the ForceImpl corresponding to this Force in a Context.

ContextImpl &	getContextImpl (Context &context)
	Get the ContextImpl corresponding to a Context.

Detailed Description

This class implements an implicit solvation force using the GB/VI model.

To use this class, create a GBVIForce object, then call addParticle() once for each particle in the System to define its parameters. The number of particles for which you define GB/VI parameters must be exactly 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().

Member Enumeration Documentation

enum BornRadiusScalingMethod

This is an enumeration of the different methods that may be used for scaling of the Born radii.

Enumerator:

NoScaling	No scaling method is applied.
QuinticSpline	Use quintic spline scaling function.

enum NonbondedMethod

This is an enumeration of the different methods that may be used for handling long range nonbonded forces.

Enumerator:

NoCutoff

No cutoff is applied to nonbonded interactions.

The full set of N^2 interactions is computed exactly. This necessarily means that periodic boundary conditions cannot be used. This is the default.

CutoffNonPeriodic

Interactions beyond the cutoff distance are ignored.

CutoffPeriodic

Periodic boundary conditions are used, so that each particle interacts only with the nearest periodic copy of each other particle.

Interactions beyond the cutoff distance are ignored.

Constructor & Destructor Documentation

GBVIForce ( )

Member Function Documentation

int addBond	(	int	particle1,
		int	particle2,
		double	distance
	)

Add a bond.

Parameters

particle1	the index of the first particle
particle2	the index of the second particle
distance	the distance between the two particles, measured in nm

Returns: the index of the bond that was added

int addParticle	(	double	charge,
		double	radius,
		double	gamma
	)

Add the GB/VI 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 GB/VI radius of the particle, measured in nm
gamma	the gamma parameter

Returns: the index of the particle that was added

ForceImpl* createImpl ( )

protectedvirtual

When a Context is created, it invokes this method on each Force in the System.

It should create a new ForceImpl object which can be used by the context for calculating forces. The ForceImpl will be deleted automatically when the Context is deleted.

Implements Force.

void getBondParameters	(	int	index,
		int &	particle1,
		int &	particle2,
		double &	distance
	)		const

Get the parameters defining a bond.

Parameters

index	the index of the bond for which to get parameters
particle1	the index of the first particle involved in the bond
particle2	the index of the second particle involved in the bond
distance	the distance between the two particles, measured in nm

BornRadiusScalingMethod getBornRadiusScalingMethod ( void ) const

Get Born radius scaling method.

double getCutoffDistance ( ) const

Get the cutoff distance (in nm) being used for nonbonded interactions.

If the NonbondedMethod in use is NoCutoff, this value will have no effect.

Returns: the cutoff distance, measured in nm

NonbondedMethod getNonbondedMethod ( ) const

Get the method used for handling long range nonbonded interactions.

int getNumBonds ( void ) const

Get number of bonds.

Returns: number of bonds

int getNumParticles ( ) const

inline

Get the number of particles in the system.

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

Get the force field parameters for a particle.

Parameters

index	the index of the particle for which to get parameters
charge	the charge of the particle, measured in units of the proton charge
radius	the GBSA radius of the particle, measured in nm
gamma	the gamma parameter

double getQuinticLowerLimitFactor ( void ) const

Get the lower limit factor used in the quintic spline scaling method (typically 0.5-0.8)

double getQuinticUpperBornRadiusLimit ( void ) const

Get the upper limit used in the quintic spline scaling method, measured in nm (~5.0)

double getSoluteDielectric ( ) const

inline

Get the dielectric constant for the solute.

double getSolventDielectric ( ) const

inline

Get the dielectric constant for the solvent.

void setBondParameters	(	int	index,
		int	particle1,
		int	particle2,
		double	bondLength
	)

Set 1-2 bonds.

Parameters

index	index of the bond for which to set parameters
particle1	index of first atom in bond
particle2	index of second atom in bond
bondLength	bond length, measured in nm

void setBornRadiusScalingMethod ( BornRadiusScalingMethod method )

Set Born radius scaling method.

void setCutoffDistance ( double distance )

Set the cutoff distance (in nm) being used for nonbonded interactions.

If the NonbondedMethod in use is NoCutoff, this value will have no effect.

Parameters

distance the cutoff distance, measured in nm

void setNonbondedMethod ( NonbondedMethod method )

Set the method used for handling long range nonbonded interactions.

void setParticleParameters	(	int	index,
		double	charge,
		double	radius,
		double	gamma
	)

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 GB/VI radius of the particle, measured in nm
gamma	the gamma parameter

void setQuinticLowerLimitFactor ( double quinticLowerLimitFactor )

Set the lower limit factor used in the quintic spline scaling method (typically 0.5-0.8)

void setQuinticUpperBornRadiusLimit ( double quinticUpperBornRadiusLimit )

Set the upper limit used in the quintic spline scaling method, measured in nm (~5.0)

void setSoluteDielectric ( double dielectric )

inline

Set the dielectric constant for the solute.

void setSolventDielectric ( double dielectric )

inline

Set the dielectric constant for the solvent.

The documentation for this class was generated from the following file:

GBVIForce.h

Public Types

Public Member Functions

Protected Member Functions

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation