This class implements an implicit solvation force using the GBSA-OBC model. More...

#include <GBSAOBCForce.h>

Inheritance diagram for GBSAOBCForce:

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...

Public Member Functions
	GBSAOBCForce ()
	Create a GBSAOBCForce. More...

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

int	addParticle (double charge, double radius, double scalingFactor)
	Add the GBSA parameters for a particle. More...

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

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

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

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

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

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

double	getSurfaceAreaEnergy () const
	Get the energy scale for the surface energy term, measured in kJ/mol/nm^2. More...

void	setSurfaceAreaEnergy (double energy)
	Set the energy scale for the surface energy term, measured in kJ/mol/nm^2. More...

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

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

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

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

void	updateParametersInContext (Context &context)
	Update the particle parameters in a Context to match those stored in this Force object. More...

bool	usesPeriodicBoundaryConditions () const
	Returns whether or not this force makes use of periodic boundary conditions. More...

Public Member Functions inherited from Force
	Force ()

virtual	~Force ()

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

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

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

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

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

Detailed Description

This class implements an implicit solvation force using the GBSA-OBC model.

To use this class, create a GBSAOBCForce object, then call addParticle() once for each particle in the System to define its parameters. The number of particles for which you define GBSA 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(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

When using this Force, the System should also include a NonbondedForce, and both objects must specify identical charges for all particles. Otherwise, the results will not be correct. Furthermore, if the nonbonded method is set to CutoffNonPeriodic or CutoffPeriodic, you should call setReactionFieldDielectric(1.0) on the NonbondedForce to turn off the reaction field approximation, which does not produce correct results when combined with GBSA.

Member Enumeration Documentation

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

GBSAOBCForce ( )

Create a GBSAOBCForce.

Member Function Documentation

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

Add the GBSA 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 GBSA radius of the particle, measured in nm
scalingFactor	the OBC scaling factor for the particle

Returns: the index of the particle that was added

ForceImpl* createImpl ( ) const

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.

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 getNumParticles ( ) const

inline

Get the number of particles in the system.

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	the charge of the particle, measured in units of the proton charge
radius	the GBSA radius of the particle, measured in nm
scalingFactor	the OBC scaling factor for the particle

double getSoluteDielectric ( ) const

inline

Get the dielectric constant for the solute.

double getSolventDielectric ( ) const

inline

Get the dielectric constant for the solvent.

double getSurfaceAreaEnergy ( ) const

inline

Get the energy scale for the surface energy term, measured in kJ/mol/nm^2.

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	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 GBSA radius of the particle, measured in nm
scalingFactor	the OBC scaling factor for the particle

void setSoluteDielectric ( double dielectric )

inline

Set the dielectric constant for the solute.

void setSolventDielectric ( double dielectric )

inline

Set the dielectric constant for the solvent.

void setSurfaceAreaEnergy ( double energy )

inline

Set the energy scale for the surface energy term, measured in kJ/mol/nm^2.

void updateParametersInContext ( Context & context )

Update the 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 nonbonded method, the cutoff distance, etc.) are unaffected and can only be changed by reinitializing the Context. Furthermore, this method cannot be used to add new particles, only to change the parameters of existing ones.

bool usesPeriodicBoundaryConditions ( ) const

inlinevirtual

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

Returns: true if force uses PBC and false otherwise

Reimplemented from Force.

References GBSAOBCForce::CutoffPeriodic.

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

GBSAOBCForce.h

Public Types

Public Member Functions

Protected Member Functions

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation