This class implements complex, multiple stage nonbonded interactions between particles. More...

#include <CustomGBForce.h>

Inheritance diagram for CustomGBForce:

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	ComputationType { SingleParticle = 0, ParticlePair = 1, ParticlePairNoExclusions = 2 }
	This is an enumeration of the different ways in which a computed value or energy term can be calculated. More...

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

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

int	getNumExclusions () const
	Get the number of particle pairs whose interactions should be excluded. More...

int	getNumPerParticleParameters () const
	Get the number of per-particle parameters that the interaction depends on. More...

int	getNumGlobalParameters () const
	Get the number of global parameters that the interaction depends on. More...

int	getNumFunctions () const
	Get the number of tabulated functions that have been defined. More...

int	getNumComputedValues () const
	Get the number of per-particle computed values the interaction depends on. More...

int	getNumEnergyTerms () const
	Get the number of terms in the energy computation. 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...

int	addPerParticleParameter (const std::string &name)
	Add a new per-particle parameter that the interaction may depend on. More...

const std::string &	getPerParticleParameterName (int index) const
	Get the name of a per-particle parameter. More...

void	setPerParticleParameterName (int index, const std::string &name)
	Set the name of a per-particle parameter. More...

int	addGlobalParameter (const std::string &name, double defaultValue)
	Add a new global parameter that the interaction may depend on. More...

const std::string &	getGlobalParameterName (int index) const
	Get the name of a global parameter. More...

void	setGlobalParameterName (int index, const std::string &name)
	Set the name of a global parameter. More...

double	getGlobalParameterDefaultValue (int index) const
	Get the default value of a global parameter. More...

void	setGlobalParameterDefaultValue (int index, double defaultValue)
	Set the default value of a global parameter. More...

int	addParticle (const std::vector< double > &parameters)
	Add the nonbonded force parameters for a particle. More...

void	getParticleParameters (int index, std::vector< double > &parameters) const
	Get the nonbonded force parameters for a particle. More...

void	setParticleParameters (int index, const std::vector< double > &parameters)
	Set the nonbonded force parameters for a particle. More...

int	addComputedValue (const std::string &name, const std::string &expression, ComputationType type)
	Add a computed value to calculate for each particle. More...

void	getComputedValueParameters (int index, std::string &name, std::string &expression, ComputationType &type) const
	Get the properties of a computed value. More...

void	setComputedValueParameters (int index, const std::string &name, const std::string &expression, ComputationType type)
	Set the properties of a computed value. More...

int	addEnergyTerm (const std::string &expression, ComputationType type)
	Add a term to the energy computation. More...

void	getEnergyTermParameters (int index, std::string &expression, ComputationType &type) const
	Get the properties of a term to the energy computation. More...

void	setEnergyTermParameters (int index, const std::string &expression, ComputationType type)
	Set the properties of a term to the energy computation. More...

int	addExclusion (int particle1, int particle2)
	Add a particle pair to the list of interactions that should be excluded. More...

void	getExclusionParticles (int index, int &particle1, int &particle2) const
	Get the particles in a pair whose interaction should be excluded. More...

void	setExclusionParticles (int index, int particle1, int particle2)
	Set the particles in a pair whose interaction should be excluded. More...

int	addFunction (const std::string &name, const std::vector< double > &values, double min, double max)
	Add a tabulated function that may appear in the energy expression. More...

void	getFunctionParameters (int index, std::string &name, std::vector< double > &values, double &min, double &max) const
	Get the parameters for a tabulated function that may appear in the energy expression. More...

void	setFunctionParameters (int index, const std::string &name, const std::vector< double > &values, double min, double max)
	Set the parameters for a tabulated function that may appear in algebraic expressions. 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 complex, multiple stage nonbonded interactions between particles.

It is designed primarily for implementing Generalized Born implicit solvation models, although it is not strictly limited to that purpose. The interaction is specified as a series of computations, each defined by an arbitrary algebraic expression. It also allows tabulated functions to be defined and used with the computations. It optionally supports periodic boundary conditions and cutoffs for long range interactions.

The computation consists of calculating some number of per-particle computed values, followed by one or more energy terms. A computed value is a scalar value that is computed for each particle in the system. It may depend on an arbitrary set of global and per-particle parameters, and well as on other computed values that have been calculated before it. Once all computed values have been calculated, the energy terms and their derivatives are evaluated to determine the system energy and particle forces. The energy terms may depend on global parameters, per-particle parameters, and per-particle computed values.

When specifying a computed value or energy term, you provide an algebraic expression to evaluate and a computation type describing how the expression is to be evaluated. There are two main types of computations:

Single Particle: The expression is evaluated once for each particle in the System. In the case of a computed value, this means the value for a particle depends only on other properties of that particle (its position, parameters, and other computed values). In the case of an energy term, it means each particle makes an independent contribution to the System energy.
Particle Pairs: The expression is evaluated for every pair of particles in the system. In the case of a computed value, the value for a particular particle is calculated by pairing it with every other particle in the system, evaluating the expression for each pair, and summing them. For an energy term, each particle pair makes an independent contribution to the System energy. (Note that energy terms are assumed to be symmetric with respect to the two interacting particles, and therefore are evaluated only once per pair. In contrast, expressions for computed values need not be symmetric and therefore are calculated twice for each pair: once when calculating the value for the first particle, and again when calculating the value for the second particle.)

Be aware that, although this class is extremely general in the computations it can define, particular Platforms may only support more restricted types of computations. In particular, all currently existing Platforms require that the first computed value must be a particle pair computation, and all computed values after the first must be single particle computations. This is sufficient for most Generalized Born models, but might not permit some other types of calculations to be implemented.

This is a complicated class to use, and an example may help to clarify it. The following code implements the OBC variant of the GB/SA solvation model, using the ACE approximation to estimate surface area:


CustomGBForce* custom = new CustomGBForce();
custom->addPerParticleParameter("q");
custom->addPerParticleParameter("radius");
custom->addPerParticleParameter("scale");
custom->addGlobalParameter("solventDielectric", obc->getSolventDielectric());
custom->addGlobalParameter("soluteDielectric", obc->getSoluteDielectric());
custom->addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(1/U^2-1/L^2)*(r-sr2*sr2/r)+0.5*log(L/U)/r+C);"
                              "U=r+sr2;"
                              "C=2*(1/or1-1/L)*step(sr2-r-or1);"
                              "L=max(or1, D);"
                              "D=abs(r-sr2);"
                              "sr2 = scale2*or2;"
                              "or1 = radius1-0.009; or2 = radius2-0.009", CustomGBForce::ParticlePairNoExclusions);
custom->addComputedValue("B", "1/(1/or-tanh(1*psi-0.8*psi^2+4.85*psi^3)/radius);"
                              "psi=I*or; or=radius-0.009", CustomGBForce::SingleParticle);
custom->addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6-0.5*138.935456*(1/soluteDielectric-1/solventDielectric)*q^2/B",
                      CustomGBForce::SingleParticle);
custom->addEnergyTerm("-138.935456*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;"
                      "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce::ParticlePair);

It begins by defining three per-particle parameters (charge, atomic radius, and scale factor) and two global parameters (the dielectric constants for the solute and solvent). It then defines a computed value "I" of type ParticlePair. The expression for evaluating it is a complicated function of the distance between each pair of particles (r), their atomic radii (radius1 and radius2), and their scale factors (scale1 and scale2). Very roughly speaking, it is a measure of the distance between each particle and other nearby particles.

Next a computation is defined for the Born Radius (B). It is computed independently for each particle, and is a function of that particle's atomic radius and the intermediate value I defined above.

Finally, two energy terms are defined. The first one is computed for each particle and represents the surface area term, as well as the self interaction part of the polarization energy. The second term is calculated for each pair of particles, and represents the screening of electrostatic interactions by the solvent.

After defining the force as shown above, you should then call addParticle() once for each particle in the System to set the values of its per-particle parameters (q, radius, and scale). The number of particles for which you set 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 parameters by calling setParticleParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

CustomGBForce also lets you specify "exclusions", particular pairs of particles whose interactions should be omitted from calculations. This is most often used for particles that are bonded to each other. Even if you specify exclusions, however, you can use the computation type ParticlePairNoExclusions to indicate that exclusions should not be applied to a particular piece of the computation.

Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, step, delta. All trigonometric functions are defined in radians, and log is the natural logarithm. step(x) = 0 if x is less than 0, 1 otherwise. delta(x) = 1 if x is 0, 0 otherwise. In expressions for particle pair calculations, the names of per-particle parameters and computed values have the suffix "1" or "2" appended to them to indicate the values for the two interacting particles. As seen in the above example, an expression may also involve intermediate quantities that are defined following the main expression, using ";" as a separator.

In addition, you can call addFunction() to define a new function based on tabulated values. You specify a vector of values, and a natural spline is created from them. That function can then appear in expressions.

Member Enumeration Documentation

enum ComputationType

This is an enumeration of the different ways in which a computed value or energy term can be calculated.

Enumerator

SingleParticle

The value is computed independently for each particle, based only on the parameters and computed values for that particle.

ParticlePair

The value is computed as a sum over all pairs of particles, except those which have been added as exclusions.

ParticlePairNoExclusions

The value is computed as a sum over all pairs of particles.

Unlike ParticlePair, the list of exclusions is ignored and all pairs are included in the sum, even those marked as exclusions.

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

CustomGBForce ( )

Create a CustomGBForce.

Member Function Documentation

int addComputedValue	(	const std::string &	name,
		const std::string &	expression,
		ComputationType	type
	)

Add a computed value to calculate for each particle.

Parameters

name	the name of the value
expression	an algebraic expression to evaluate when calculating the computed value. If the ComputationType is SingleParticle, the expression is evaluated independently for each particle, and may depend on its x, y, and z coordinates, as well as the per-particle parameters and previous computed values for that particle. If the ComputationType is ParticlePair or ParticlePairNoExclusions, the expression is evaluated once for every other particle in the system and summed to get the final value. In the latter case, the expression may depend on the distance r between the two particles, and on the per-particle parameters and previous computed values for each of them. Append "1" to a variable name to indicate the parameter for the particle whose value is being calculated, and "2" to indicate the particle it is interacting with.
type	the method to use for computing this value

int addEnergyTerm	(	const std::string &	expression,
		ComputationType	type
	)

Add a term to the energy computation.

Parameters

expression an algebraic expression to evaluate when calculating the energy. If the ComputationType is SingleParticle, the expression is evaluated once for each particle, and may depend on its x, y, and z coordinates, as well as the per-particle parameters and computed values for that particle. If the ComputationType is ParticlePair or ParticlePairNoExclusions, the expression is evaluated once for every pair of particles in the system. In the latter case, the expression may depend on the distance r between the two particles, and on the per-particle parameters and computed values for each of them. Append "1" to a variable name to indicate the parameter for the first particle in the pair and "2" to indicate the second particle in the pair.

type the method to use for computing this value

int addExclusion	(	int	particle1,
		int	particle2
	)

Add a particle pair to the list of interactions that should be excluded.

Parameters

particle1	the index of the first particle in the pair
particle2	the index of the second particle in the pair

Returns: the index of the exclusion that was added

int addFunction	(	const std::string &	name,
		const std::vector< double > &	values,
		double	min,
		double	max
	)

Add a tabulated function that may appear in the energy expression.

Parameters

name	the name of the function as it appears in expressions
values	the tabulated values of the function f(x) at uniformly spaced values of x between min and max. The function is assumed to be zero for x < min or x > max.
min	the value of the independent variable corresponding to the first element of values
max	the value of the independent variable corresponding to the last element of values

Returns: the index of the function that was added

int addGlobalParameter	(	const std::string &	name,
		double	defaultValue
	)

Add a new global parameter that the interaction may depend on.

Parameters

name	the name of the parameter
defaultValue	the default value of the parameter

Returns: the index of the parameter that was added

int addParticle ( const std::vector< double > & parameters )

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.

Parameters

parameters the list of parameters for the new particle

Returns: the index of the particle that was added

int addPerParticleParameter ( const std::string & name )

Add a new per-particle parameter that the interaction may depend on.

Parameters

name	the name of the parameter

Returns: the index of the parameter 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.

void getComputedValueParameters	(	int	index,
		std::string &	name,
		std::string &	expression,
		ComputationType &	type
	)		const

Get the properties of a computed value.

Parameters

index	the index of the computed value for which to get parameters
name	the name of the value
expression	an algebraic expression to evaluate when calculating the computed value. If the ComputationType is SingleParticle, the expression is evaluated independently for each particle, and may depend on its x, y, and z coordinates, as well as the per-particle parameters and previous computed values for that particle. If the ComputationType is ParticlePair or ParticlePairNoExclusions, the expression is evaluated once for every other particle in the system and summed to get the final value. In the latter case, the expression may depend on the distance r between the two particles, and on the per-particle parameters and previous computed values for each of them. Append "1" to a variable name to indicate the parameter for the particle whose value is being calculated, and "2" to indicate the particle it is interacting with.
type	the method to use for computing this value

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

void getEnergyTermParameters	(	int	index,
		std::string &	expression,
		ComputationType &	type
	)		const

Get the properties of a term to the energy computation.

Parameters

index	the index of the term for which to get parameters
expression	an algebraic expression to evaluate when calculating the energy. If the ComputationType is SingleParticle, the expression is evaluated once for each particle, and may depend on its x, y, and z coordinates, as well as the per-particle parameters and computed values for that particle. If the ComputationType is ParticlePair or ParticlePairNoExclusions, the expression is evaluated once for every pair of particles in the system. In the latter case, the expression may depend on the distance r between the two particles, and on the per-particle parameters and computed values for each of them. Append "1" to a variable name to indicate the parameter for the first particle in the pair and "2" to indicate the second particle in the pair.
type	the method to use for computing this value

void getExclusionParticles	(	int	index,
		int &	particle1,
		int &	particle2
	)		const

Get the particles in a pair whose interaction should be excluded.

Parameters

index	the index of the exclusion for which to get particle indices
particle1	the index of the first particle in the pair
particle2	the index of the second particle in the pair

void getFunctionParameters	(	int	index,
		std::string &	name,
		std::vector< double > &	values,
		double &	min,
		double &	max
	)		const

Get the parameters for a tabulated function that may appear in the energy expression.

Parameters

index	the index of the function for which to get parameters
name	the name of the function as it appears in expressions
values	the tabulated values of the function f(x) at uniformly spaced values of x between min and max. The function is assumed to be zero for x < min or x > max.
min	the value of the independent variable corresponding to the first element of values
max	the value of the independent variable corresponding to the last element of values

double getGlobalParameterDefaultValue ( int index ) const

Get the default value of a global parameter.

Parameters

index the index of the parameter for which to get the default value

Returns: the parameter default value

const std::string& getGlobalParameterName ( int index ) const

Get the name of a global parameter.

Parameters

index the index of the parameter for which to get the name

Returns: the parameter name

NonbondedMethod getNonbondedMethod ( ) const

Get the method used for handling long range nonbonded interactions.

int getNumComputedValues ( ) const

inline

Get the number of per-particle computed values the interaction depends on.

int getNumEnergyTerms ( ) const

inline

Get the number of terms in the energy computation.

int getNumExclusions ( ) const

inline

Get the number of particle pairs whose interactions should be excluded.

int getNumFunctions ( ) const

inline

Get the number of tabulated functions that have been defined.

int getNumGlobalParameters ( ) const

inline

Get the number of global parameters that the interaction depends on.

int getNumParticles ( ) const

inline

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

int getNumPerParticleParameters ( ) const

inline

Get the number of per-particle parameters that the interaction depends on.

void getParticleParameters	(	int	index,
		std::vector< double > &	parameters
	)		const

Get the nonbonded force parameters for a particle.

Parameters

index	the index of the particle for which to get parameters
parameters	the list of parameters for the specified particle

const std::string& getPerParticleParameterName ( int index ) const

Get the name of a per-particle parameter.

Parameters

index the index of the parameter for which to get the name

Returns: the parameter name

void setComputedValueParameters	(	int	index,
		const std::string &	name,
		const std::string &	expression,
		ComputationType	type
	)

Set the properties of a computed value.

Parameters

index	the index of the computed value for which to set parameters
name	the name of the value
expression	an algebraic expression to evaluate when calculating the computed value. If the ComputationType is SingleParticle, the expression is evaluated independently for each particle, and may depend on its x, y, and z coordinates, as well as the per-particle parameters and previous computed values for that particle. If the ComputationType is ParticlePair or ParticlePairNoExclusions, the expression is evaluated once for every other particle in the system and summed to get the final value. In the latter case, the expression may depend on the distance r between the two particles, and on the per-particle parameters and previous computed values for each of them. Append "1" to a variable name to indicate the parameter for the particle whose value is being calculated, and "2" to indicate the particle it is interacting with.
type	the method to use for computing this value

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 setEnergyTermParameters	(	int	index,
		const std::string &	expression,
		ComputationType	type
	)

Set the properties of a term to the energy computation.

Parameters

index	the index of the term for which to set parameters
expression	an algebraic expression to evaluate when calculating the energy. If the ComputationType is SingleParticle, the expression is evaluated once for each particle, and may depend on its x, y, and z coordinates, as well as the per-particle parameters and computed values for that particle. If the ComputationType is ParticlePair or ParticlePairNoExclusions, the expression is evaluated once for every pair of particles in the system. In the latter case, the expression may depend on the distance r between the two particles, and on the per-particle parameters and computed values for each of them. Append "1" to a variable name to indicate the parameter for the first particle in the pair and "2" to indicate the second particle in the pair.
type	the method to use for computing this value

void setExclusionParticles	(	int	index,
		int	particle1,
		int	particle2
	)

Set the particles in a pair whose interaction should be excluded.

Parameters

index	the index of the exclusion for which to set particle indices
particle1	the index of the first particle in the pair
particle2	the index of the second particle in the pair

void setFunctionParameters	(	int	index,
		const std::string &	name,
		const std::vector< double > &	values,
		double	min,
		double	max
	)

Set the parameters for a tabulated function that may appear in algebraic expressions.

Parameters

index	the index of the function for which to set parameters
name	the name of the function as it appears in expressions
values	the tabulated values of the function f(x) at uniformly spaced values of x between min and max. The function is assumed to be zero for x < min or x > max.
min	the value of the independent variable corresponding to the first element of values
max	the value of the independent variable corresponding to the last element of values

void setGlobalParameterDefaultValue	(	int	index,
		double	defaultValue
	)

Set the default value of a global parameter.

Parameters

index	the index of the parameter for which to set the default value
name	the default value of the parameter

void setGlobalParameterName	(	int	index,
		const std::string &	name
	)

Set the name of a global parameter.

Parameters

index	the index of the parameter for which to set the name
name	the name of the parameter

void setNonbondedMethod ( NonbondedMethod method )

Set the method used for handling long range nonbonded interactions.

void setParticleParameters	(	int	index,
		const std::vector< double > &	parameters
	)

Set the nonbonded force parameters for a particle.

Parameters

index	the index of the particle for which to set parameters
parameters	the list of parameters for the specified particle

void setPerParticleParameterName	(	int	index,
		const std::string &	name
	)

Set the name of a per-particle parameter.

Parameters

index	the index of the parameter for which to set the name
name	the name of the parameter

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.

This method has several limitations. The only information it updates is the values of per-particle parameters. All other aspects of the Force (such as the energy function) are unaffected and can only be changed by reinitializing the Context. Also, this method cannot be used to add new particles, only to change the parameters of existing ones.

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

CustomGBForce.h

Public Types

Public Member Functions

Protected Member Functions

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation