This class implements a buffered 14-7 potential used to model van der Waals forces. More...

#include <AmoebaVdwForce.h>

Inheritance diagram for AmoebaVdwForce:

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

Public Member Functions
	AmoebaVdwForce ()
	Create an Amoeba VdwForce. More...

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

void	setParticleParameters (int particleIndex, int parentIndex, double sigma, double epsilon, double reductionFactor)
	Set the force field parameters for a vdw particle. More...

void	getParticleParameters (int particleIndex, int &parentIndex, double &sigma, double &epsilon, double &reductionFactor) const
	Get the force field parameters for a vdw particle. More...

int	addParticle (int parentIndex, double sigma, double epsilon, double reductionFactor)
	Add the force field parameters for a vdw particle. More...

void	setSigmaCombiningRule (const std::string &sigmaCombiningRule)
	Set sigma combining rule. More...

const std::string &	getSigmaCombiningRule (void) const
	Get sigma combining rule. More...

void	setEpsilonCombiningRule (const std::string &epsilonCombiningRule)
	Set epsilon combining rule. More...

const std::string &	getEpsilonCombiningRule (void) const
	Get epsilon combining rule. More...

bool	getUseDispersionCorrection () const
	Get whether to add a contribution to the energy that approximately represents the effect of VdW interactions beyond the cutoff distance. More...

void	setUseDispersionCorrection (bool useCorrection)
	Set whether to add a contribution to the energy that approximately represents the effect of VdW interactions beyond the cutoff distance. More...

void	setParticleExclusions (int particleIndex, const std::vector< int > &exclusions)
	Set exclusions for specified particle. More...

void	getParticleExclusions (int particleIndex, std::vector< int > &exclusions) const
	Get exclusions for specified particle. More...

void	setCutoff (double cutoff)
	Set the cutoff distance. More...

double	getCutoff () const
	Get the cutoff distance. 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...

void	updateParametersInContext (Context &context)
	Update the per-particle parameters in a Context to match those stored in this Force object. 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 a buffered 14-7 potential used to model van der Waals forces.

To use it, create an AmoebaVdwForce object then call addParticle() once for each particle. 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().

A unique feature of this class is that the interaction site for a particle does not need to be exactly at the particle's location. Instead, it can be placed a fraction of the distance from that particle to another one. This is typically done for hydrogens to place the interaction site slightly closer to the parent atom. The fraction is known as the "reduction factor", since it reduces the distance from the parent atom to the interaction site.

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.

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

AmoebaVdwForce ( )

Create an Amoeba VdwForce.

Member Function Documentation

int addParticle	(	int	parentIndex,
		double	sigma,
		double	epsilon,
		double	reductionFactor
	)

Add the force field parameters for a vdw particle.

Parameters

parentIndex	the index of the parent particle
sigma	vdw sigma
epsilon	vdw epsilon
reductionFactor	the fraction of the distance along the line from the parent particle to this particle at which the interaction site should be placed

Returns: index of added particle

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 getCutoff ( ) const

Get the cutoff distance.

const std::string& getEpsilonCombiningRule ( void ) const

Get epsilon combining rule.

Returns: epsilonCombiningRule epsilon combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'HARMONIC', 'HHG'

NonbondedMethod getNonbondedMethod ( ) const

Get the method used for handling long range nonbonded interactions.

int getNumParticles ( ) const

inline

Get the number of particles.

void getParticleExclusions	(	int	particleIndex,
		std::vector< int > &	exclusions
	)		const

Get exclusions for specified particle.

Parameters

particleIndex	particle index
exclusions	vector of exclusions

void getParticleParameters	(	int	particleIndex,
		int &	parentIndex,
		double &	sigma,
		double &	epsilon,
		double &	reductionFactor
	)		const

Get the force field parameters for a vdw particle.

Parameters

particleIndex	the particle index
parentIndex	the index of the parent particle
sigma	vdw sigma
epsilon	vdw epsilon
reductionFactor	the fraction of the distance along the line from the parent particle to this particle at which the interaction site should be placed

const std::string& getSigmaCombiningRule ( void ) const

Get sigma combining rule.

Returns: sigmaCombiningRule sigma combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'CUBIC-MEAN'

bool getUseDispersionCorrection ( ) const

inline

Get whether to add a contribution to the energy that approximately represents the effect of VdW interactions beyond the cutoff distance.

The energy depends on the volume of the periodic box, and is only applicable when periodic boundary conditions are used. When running simulations at constant pressure, adding this contribution can improve the quality of results.

void setCutoff ( double cutoff )

Set the cutoff distance.

void setEpsilonCombiningRule ( const std::string & epsilonCombiningRule )

Set epsilon combining rule.

Parameters

epsilonCombiningRule epsilon combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'HARMONIC', 'HHG'

void setNonbondedMethod ( NonbondedMethod method )

Set the method used for handling long range nonbonded interactions.

void setParticleExclusions	(	int	particleIndex,
		const std::vector< int > &	exclusions
	)

Set exclusions for specified particle.

Parameters

particleIndex	particle index
exclusions	vector of exclusions

void setParticleParameters	(	int	particleIndex,
		int	parentIndex,
		double	sigma,
		double	epsilon,
		double	reductionFactor
	)

Set the force field parameters for a vdw particle.

Parameters

particleIndex	the particle index
parentIndex	the index of the parent particle
sigma	vdw sigma
epsilon	vdw epsilon
reductionFactor	the fraction of the distance along the line from the parent particle to this particle at which the interaction site should be placed

void setSigmaCombiningRule ( const std::string & sigmaCombiningRule )

Set sigma combining rule.

Parameters

sigmaCombiningRule sigma combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'CUBIC-MEAN'

void setUseDispersionCorrection ( bool useCorrection )

inline

Set whether to add a contribution to the energy that approximately represents the effect of VdW interactions beyond the cutoff distance.

The energy depends on the volume of the periodic box, and is only applicable when periodic boundary conditions are used. When running simulations at constant pressure, adding this contribution can improve the quality of results.

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 updateParametersInState() 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.

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

AmoebaVdwForce.h

Public Types

Public Member Functions

Protected Member Functions

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation