GBVIForce Class Reference

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

#include <GBVIForce.h>

Inheritance diagram for GBVIForce:

Classes
class	BondInfo
	This is an internal class used to record information about a bond.
class	ParticleInfo
	This is an internal class used to record information about a particle.
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
	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.
Protected Member Functions
ForceImpl *	createImpl ()
	When a Context is created, it invokes this method on each Force in the System.

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 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 ( ) [protected, virtual]

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

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 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

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 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

GBVIForce Class Reference

Classes

Public Types

Public Member Functions

Protected Member Functions

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation