This class implements nonbonded interactions between particles, including a Coulomb force to represent electrostatics and a Lennard-Jones force to represent van der Waals interactions. More...

#include <NonbondedForce.h>

Inheritance diagram for NonbondedForce:

Public Types
enum	NonbondedMethod { NoCutoff = 0, CutoffNonPeriodic = 1, CutoffPeriodic = 2, Ewald = 3, PME = 4 }
	This is an enumeration of the different methods that may be used for handling long range nonbonded forces. More...

Public Member Functions
	NonbondedForce ()
	Create a NonbondedForce.

int	getNumParticles () const
	Get the number of particles for which force field parameters have been defined.

int	getNumExceptions () const
	Get the number of special interactions that should be calculated differently from other interactions.

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.

double	getReactionFieldDielectric () const
	Get the dielectric constant to use for the solvent in the reaction field approximation.

void	setReactionFieldDielectric (double dielectric)
	Set the dielectric constant to use for the solvent in the reaction field approximation.

double	getEwaldErrorTolerance () const
	Get the error tolerance for Ewald summation.

void	setEwaldErrorTolerance (double tol)
	Get the error tolerance for Ewald summation.

int	addParticle (double charge, double sigma, double epsilon)
	Add the nonbonded force parameters for a particle.

void	getParticleParameters (int index, double &charge, double &sigma, double &epsilon) const
	Get the nonbonded force parameters for a particle.

void	setParticleParameters (int index, double charge, double sigma, double epsilon)
	Set the nonbonded force parameters for a particle.

int	addException (int particle1, int particle2, double chargeProd, double sigma, double epsilon, bool replace=false)
	Add an interaction to the list of exceptions that should be calculated differently from other interactions.

void	getExceptionParameters (int index, int &particle1, int &particle2, double &chargeProd, double &sigma, double &epsilon) const
	Get the force field parameters for an interaction that should be calculated differently from others.

void	setExceptionParameters (int index, int particle1, int particle2, double chargeProd, double sigma, double epsilon)
	Set the force field parameters for an interaction that should be calculated differently from others.

void	createExceptionsFromBonds (const std::vector< std::pair< int, int > > &bonds, double coulomb14Scale, double lj14Scale)
	Identify exceptions based on the molecular topology.

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

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

int	getReciprocalSpaceForceGroup () const
	Get the force group that reciprocal space interactions for Ewald or PME are included in.

void	setReciprocalSpaceForceGroup (int group)
	Set the force group that reciprocal space interactions for Ewald or PME are included in.

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

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 nonbonded interactions between particles, including a Coulomb force to represent electrostatics and a Lennard-Jones force to represent van der Waals interactions.

It optionally supports periodic boundary conditions and cutoffs for long range interactions. Lennard-Jones interactions are calculated with the Lorentz-Bertelot combining rule: it uses the arithmetic mean of the sigmas and the geometric mean of the epsilons for the two interacting particles.

To use this class, create a NonbondedForce object, then call addParticle() once for each particle in the System to define its parameters. The number of particles for which you define nonbonded 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().

NonbondedForce also lets you specify "exceptions", particular pairs of particles whose interactions should be computed based on different parameters than those defined for the individual particles. This can be used to completely exclude certain interactions from the force calculation, or to alter how they interact with each other.

Many molecular force fields omit Coulomb and Lennard-Jones interactions between particles separated by one or two bonds, while using modified parameters for those separated by three bonds (known as "1-4 interactions"). This class provides a convenience method for this case called createExceptionsFromBonds(). You pass to it a list of bonds and the scale factors to use for 1-4 interactions. It identifies all pairs of particles which are separated by 1, 2, or 3 bonds, then automatically creates exceptions for them.

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. Coulomb interactions closer than the cutoff distance are modified using the reaction field method.
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. Coulomb interactions closer than the cutoff distance are modified using the reaction field method.
Ewald	Periodic boundary conditions are used, and Ewald summation is used to compute the interaction of each particle with all periodic copies of every other particle.
PME	Periodic boundary conditions are used, and Particle-Mesh Ewald (PME) summation is used to compute the interaction of each particle with all periodic copies of every other particle.

Constructor & Destructor Documentation

NonbondedForce ( )

Create a NonbondedForce.

Member Function Documentation

int addException	(	int	particle1,
		int	particle2,
		double	chargeProd,
		double	sigma,
		double	epsilon,
		bool	replace = `false`
	)

Add an interaction to the list of exceptions that should be calculated differently from other interactions.

If chargeProd and epsilon are both equal to 0, this will cause the interaction to be completely omitted from force and energy calculations.

In many cases, you can use createExceptionsFromBonds() rather than adding each exception explicitly.

Parameters

particle1	the index of the first particle involved in the interaction
particle2	the index of the second particle involved in the interaction
chargeProd	the scaled product of the atomic charges (i.e. the strength of the Coulomb interaction), measured in units of the proton charge squared
sigma	the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
epsilon	the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol
replace	determines the behavior if there is already an exception for the same two particles. If true, the existing one is replaced. If false, an exception is thrown.

Returns: the index of the exception that was added

int addParticle	(	double	charge,
		double	sigma,
		double	epsilon
	)

Add the nonbonded force 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 calculating the Lennard-Jones interaction between two particles, the arithmetic mean of the sigmas and the geometric mean of the epsilons for the two interacting particles is used (the Lorentz-Bertelot combining rule).

Parameters

charge	the charge of the particle, measured in units of the proton charge
sigma	the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
epsilon	the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol

Returns: the index of the particle that was added

void createExceptionsFromBonds	(	const std::vector< std::pair< int, int > > &	bonds,
		double	coulomb14Scale,
		double	lj14Scale
	)

Identify exceptions based on the molecular topology.

Particles which are separated by one or two bonds are set to not interact at all, while pairs of particles separated by three bonds (known as "1-4 interactions") have their Coulomb and Lennard-Jones interactions reduced by a fixed factor.

Parameters

bonds	the set of bonds based on which to construct exceptions. Each element specifies the indices of two particles that are bonded to each other.
coulomb14Scale	pairs of particles separated by three bonds will have the strength of their Coulomb interaction multiplied by this factor
lj14Scale	pairs of particles separated by three bonds will have the strength of their Lennard-Jones interaction multiplied by this factor

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.

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

double getEwaldErrorTolerance ( ) const

Get the error tolerance for Ewald summation.

This corresponds to the fractional error in the forces which is acceptable. This value is used to select the reciprocal space cutoff and separation parameter so that the average error level will be less than the tolerance. There is not a rigorous guarantee that all forces on all atoms will be less than the tolerance, however.

void getExceptionParameters	(	int	index,
		int &	particle1,
		int &	particle2,
		double &	chargeProd,
		double &	sigma,
		double &	epsilon
	)		const

Get the force field parameters for an interaction that should be calculated differently from others.

Parameters

index	the index of the interaction for which to get parameters
particle1	the index of the first particle involved in the interaction
particle2	the index of the second particle involved in the interaction
chargeProd	the scaled product of the atomic charges (i.e. the strength of the Coulomb interaction), measured in units of the proton charge squared
sigma	the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
epsilon	the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol

NonbondedMethod getNonbondedMethod ( ) const

Get the method used for handling long range nonbonded interactions.

int getNumExceptions ( ) const

inline

Get the number of special interactions that should be calculated differently from other interactions.

int getNumParticles ( ) const

inline

Get the number of particles for which force field parameters have been defined.

void getParticleParameters	(	int	index,
		double &	charge,
		double &	sigma,
		double &	epsilon
	)		const

Get the nonbonded force 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
sigma	the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
epsilon	the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol

double getReactionFieldDielectric ( ) const

Get the dielectric constant to use for the solvent in the reaction field approximation.

int getReciprocalSpaceForceGroup ( ) const

Get the force group that reciprocal space interactions for Ewald or PME are included in.

This allows multiple time step integrators to evaluate direct and reciprocal space interactions at different intervals: getForceGroup() specifies the group for direct space, and getReciprocalSpaceForceGroup() specifies the group for reciprocal space. If this is -1 (the default value), the same force group is used for reciprocal space as for direct space.

bool getUseDispersionCorrection ( ) const

inline

Get whether to add a contribution to the energy that approximately represents the effect of Lennard-Jones 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 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 setEwaldErrorTolerance ( double tol )

Get the error tolerance for Ewald summation.

This corresponds to the fractional error in the forces which is acceptable. This value is used to select the reciprocal space cutoff and separation parameter so that the average error level will be less than the tolerance. There is not a rigorous guarantee that all forces on all atoms will be less than the tolerance, however.

void setExceptionParameters	(	int	index,
		int	particle1,
		int	particle2,
		double	chargeProd,
		double	sigma,
		double	epsilon
	)

Set the force field parameters for an interaction that should be calculated differently from others.

If chargeProd and epsilon are both equal to 0, this will cause the interaction to be completely omitted from force and energy calculations.

Parameters

index	the index of the interaction for which to get parameters
particle1	the index of the first particle involved in the interaction
particle2	the index of the second particle involved in the interaction
chargeProd	the scaled product of the atomic charges (i.e. the strength of the Coulomb interaction), measured in units of the proton charge squared
sigma	the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
epsilon	the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol

void setNonbondedMethod ( NonbondedMethod method )

Set the method used for handling long range nonbonded interactions.

void setParticleParameters	(	int	index,
		double	charge,
		double	sigma,
		double	epsilon
	)

Set the nonbonded force parameters for a particle.

When calculating the Lennard-Jones interaction between two particles, it uses the arithmetic mean of the sigmas and the geometric mean of the epsilons for the two interacting particles (the Lorentz-Bertelot combining rule).

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
sigma	the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
epsilon	the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol

void setReactionFieldDielectric ( double dielectric )

Set the dielectric constant to use for the solvent in the reaction field approximation.

void setReciprocalSpaceForceGroup ( int group )

Set the force group that reciprocal space interactions for Ewald or PME are included in.

This allows multiple time step integrators to evaluate direct and reciprocal space interactions at different intervals: setForceGroup() specifies the group for direct space, and setReciprocalSpaceForceGroup() specifies the group for reciprocal space. If this is -1 (the default value), the same force group is used for reciprocal space as for direct space.

Parameters

group the group index. Legal values are between 0 and 31 (inclusive), or -1 to use the same force group that is specified for direct space.

void setUseDispersionCorrection ( bool useCorrection )

inline

Set whether to add a contribution to the energy that approximately represents the effect of Lennard-Jones 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 particle and exception 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() and setExceptionParameters() to modify this object's parameters, then call updateParametersInState() to copy them over to the Context.

This method has several limitations. The only information it updates is the parameters of particles and exceptions. 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, only the chargeProd, sigma, and epsilon values of an exception can be changed; the pair of particles involved in the exception cannot change. Finally, this method cannot be used to add new particles or exceptions, only to change the parameters of existing ones.

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

NonbondedForce.h

Public Types

Public Member Functions

Protected Member Functions

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation