CustomHbondForce Class Reference

This class supports a wide variety of energy functions used to represent hydrogen bonding. More...

#include <CustomHbondForce.h>

Inheritance diagram for CustomHbondForce:

List of all members.

Classes
class	ExclusionInfo
	This is an internal class used to record information about an exclusion.
class	FunctionInfo
	This is an internal class used to record information about a tabulated function.
class	GlobalParameterInfo
	This is an internal class used to record information about a global parameter.
class	GroupInfo
	This is an internal class used to record information about a donor or acceptor.
class	PerPairParameterInfo
	This is an internal class used to record information about a per-donor or per-acceptor parameter.
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
	CustomHbondForce (const std::string &energy)
	Create a CustomHbondForce.
int	getNumDonors () const
	Get the number of donors for which force field parameters have been defined.
int	getNumAcceptors () const
	Get the number of acceptors for which force field parameters have been defined.
int	getNumExclusions () const
	Get the number of donor-acceptor pairs whose interactions should be excluded.
int	getNumPerDonorParameters () const
	Get the number of per-donor parameters that the interaction depends on.
int	getNumPerAcceptorParameters () const
	Get the number of per-acceptor parameters that the interaction depends on.
int	getNumGlobalParameters () const
	Get the number of global parameters that the interaction depends on.
int	getNumFunctions () const
	Get the number of tabulated functions that have been defined.
const std::string &	getEnergyFunction () const
	Get the algebraic expression that gives the interaction energy between a donor and an acceptor.
void	setEnergyFunction (const std::string &energy)
	Set the algebraic expression that gives the interaction energy between a donor and an acceptor.
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.
void	setCutoffDistance (double distance)
	Set the cutoff distance (in nm) being used.
int	addPerDonorParameter (const std::string &name)
	Add a new per-donor parameter that the interaction may depend on.
const std::string &	getPerDonorParameterName (int index) const
	Get the name of a per-donor parameter.
void	setPerDonorParameterName (int index, const std::string &name)
	Set the name of a per-donor parameter.
int	addPerAcceptorParameter (const std::string &name)
	Add a new per-acceptor parameter that the interaction may depend on.
const std::string &	getPerAcceptorParameterName (int index) const
	Get the name of a per-acceptor parameter.
void	setPerAcceptorParameterName (int index, const std::string &name)
	Set the name of a per-acceptor parameter.
int	addGlobalParameter (const std::string &name, double defaultValue)
	Add a new global parameter that the interaction may depend on.
const std::string &	getGlobalParameterName (int index) const
	Get the name of a global parameter.
void	setGlobalParameterName (int index, const std::string &name)
	Set the name of a global parameter.
double	getGlobalParameterDefaultValue (int index) const
	Get the default value of a global parameter.
void	setGlobalParameterDefaultValue (int index, double defaultValue)
	Set the default value of a global parameter.
int	addDonor (int d1, int d2, int d3, const std::vector< double > &parameters)
	Add a donor group to the force.
void	getDonorParameters (int index, int &d1, int &d2, int &d3, std::vector< double > &parameters) const
	Get the properties of a donor group.
void	setDonorParameters (int index, int d1, int d2, int d3, const std::vector< double > &parameters)
	Set the properties of a donor group.
int	addAcceptor (int a1, int a2, int a3, const std::vector< double > &parameters)
	Add an acceptor group to the force.
void	getAcceptorParameters (int index, int &a1, int &a2, int &a3, std::vector< double > &parameters) const
	Get the properties of an acceptor group.
void	setAcceptorParameters (int index, int a1, int a2, int a3, const std::vector< double > &parameters)
	Set the properties of an acceptor group.
int	addExclusion (int donor, int acceptor)
	Add a donor-acceptor pair to the list of interactions that should be excluded.
void	getExclusionParticles (int index, int &donor, int &acceptor) const
	Get the donor and acceptor in a pair whose interaction should be excluded.
void	setExclusionParticles (int index, int donor, int acceptor)
	Get the donor and acceptor in a pair whose interaction should be excluded.
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.
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.
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.
Protected Member Functions
ForceImpl *	createImpl ()
	When a Context is created, it invokes this method on each Force in the System.

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Detailed Description

This class supports a wide variety of energy functions used to represent hydrogen bonding.

It computes interactions between "donor" particle groups and "acceptor" particle groups, where each group may include up to three particles. Typically a donor group consists of a hydrogen atom and the atoms it is bonded to, and an acceptor group consists of a negatively charged atom and the atoms it is bonded to.

We refer to the particles in a donor group as d1, d2 and d3, and the particles in an acceptor group as a1, a2, and a3. For each donor and each acceptor, CustomHbondForce evaluates a user supplied algebraic expression to determine the interaction energy. The expression may depend on arbitrary distances, angles, and dihedral angles defined by any of the six particles involved. The function distance(p1, p2) is the distance between the particles p1 and p2 (where "p1" and "p2" should be replaced by the names of the actual particles to calculate the distance between), angle(p1, p2, p3) is the angle formed by the three specified particles, and dihedral(p1, p2, p3, p4) is the dihedral angle formed by the four specified particles.

The expression also may involve tabulated functions, and may depend on arbitrary global, per-donor, and per-acceptor parameters. It also optionally supports periodic boundary conditions and cutoffs for long range interactions.

To use this class, create a CustomHbondForce object, passing an algebraic expression to the constructor that defines the interaction energy between each donor and acceptor. Then call addPerDonorParameter() to define per-donor parameters, addPerAcceptorParameter() to define per-acceptor parameters, and addGlobalParameter() to define global parameters. The values of per-donor and per-acceptor parameters are specified as part of the system definition, while values of global parameters may be modified during a simulation by calling Context::setParameter().

Next, call addDonor() and addAcceptor() to define donors and acceptors and specify their parameter values. After a donor or acceptor has been added, you can modify its parameters by calling setDonorParameters() or setAcceptorParameters().

CustomHbondForce also lets you specify "exclusions", particular combinations of donors and acceptors whose interactions should be omitted from force and energy calculations. This is most often used for particles that are bonded to each other.

As an example, the following code creates a CustomHbondForce that implements a simple harmonic potential to keep the distance between a1 and d1, and the angle formed by a1-d1-d2, near ideal values:

CustomHbondForce* force = new CustomHbondForce("k*(distance(a1,d1)-r0)^2*(angle(a1,d1,d2)-theta0)^2");

This force depends on three parameters: k, r0, and theta0. The following code defines these as per-donor parameters:

 force->addPerDonorParameter("k");
 force->addPerDonorParameter("r0");
 force->addPerDonorParameter("theta0");
 

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. All trigonometric functions are defined in radians, and log is the natural logarithm. step(x) = 0 if x is less than 0, 1 otherwise.

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 the expression.

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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.

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Constructor & Destructor Documentation

CustomHbondForce

(

const std::string &

energy

)

[explicit]

Create a CustomHbondForce.

Parameters:

energy

an algebraic expression giving the interaction energy between a donor as a function of inter-particle distances, angles, and dihedrals, as well as any global, per-donor, and per-acceptor parameters

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Member Function Documentation

int addAcceptor	(	int	a1,
		int	a2,
		int	a3,
		const std::vector< double > &	parameters
	)

Add an acceptor group to the force.

Parameters:

	a1	the index of the first particle for this acceptor group
	a2	the index of the second particle for this acceptor group. If the group only includes one particle, this must be -1.
	a3	the index of the third particle for this acceptor group. If the group includes less than three particles, this must be -1.
	parameters	the list of per-acceptor parameter values for the new acceptor

Returns:

the index of the acceptor that was added

int addDonor	(	int	d1,
		int	d2,
		int	d3,
		const std::vector< double > &	parameters
	)

Add a donor group to the force.

Parameters:

	d1	the index of the first particle for this donor group
	d2	the index of the second particle for this donor group. If the group only includes one particle, this must be -1.
	d3	the index of the third particle for this donor group. If the group includes less than three particles, this must be -1.
	parameters	the list of per-donor parameter values for the new donor

Returns:

the index of the donor that was added

int addExclusion	(	int	donor,
		int	acceptor
	)

Add a donor-acceptor pair to the list of interactions that should be excluded.

Parameters:

	donor	the index of the donor to exclude
	acceptor	the index of the acceptor to exclude

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 addPerAcceptorParameter

(

const std::string &

name

)

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

Parameters:

name

the name of the parameter

Returns:

the index of the parameter that was added

int addPerDonorParameter

(

const std::string &

name

)

Add a new per-donor 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

(

)

[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 getAcceptorParameters	(	int	index,
		int &	a1,
		int &	a2,
		int &	a3,
		std::vector< double > &	parameters
	)			const

Get the properties of an acceptor group.

Parameters:

	index	the index of the acceptor group to get
	a1	the index of the first particle for this acceptor group
	a2	the index of the second particle for this acceptor group. If the group only includes one particle, this will be -1.
	a3	the index of the third particle for this acceptor group. If the group includes less than three particles, this will be -1.
	parameters	the list of per-acceptor parameter values for the new acceptor

double getCutoffDistance

(

)

const

Get the cutoff distance (in nm) being used.

All interactions for which the distance between d1 and a1 is greater than the cutoff will be ignored. If the NonbondedMethod in use is NoCutoff, this value will have no effect.

Returns:

the cutoff distance, measured in nm

void getDonorParameters	(	int	index,
		int &	d1,
		int &	d2,
		int &	d3,
		std::vector< double > &	parameters
	)			const

Get the properties of a donor group.

Parameters:

	index	the index of the donor group to get
	d1	the index of the first particle for this donor group
	d2	the index of the second particle for this donor group. If the group only includes one particle, this will be -1.
	d3	the index of the third particle for this donor group. If the group includes less than three particles, this will be -1.
	parameters	the list of per-donor parameter values for the new donor

const std::string& getEnergyFunction

(

)

const

Get the algebraic expression that gives the interaction energy between a donor and an acceptor.

void getExclusionParticles	(	int	index,
		int &	donor,
		int &	acceptor
	)			const

Get the donor and acceptor in a pair whose interaction should be excluded.

Parameters:

	index	the index of the exclusion for which to get donor and acceptor indices
	particle1	the index of the donor
	particle2	the index of the acceptor

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 getNumAcceptors

(

)

const [inline]

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

int getNumDonors

(

)

const [inline]

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

int getNumExclusions

(

)

const [inline]

Get the number of donor-acceptor 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 getNumPerAcceptorParameters

(

)

const [inline]

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

int getNumPerDonorParameters

(

)

const [inline]

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

const std::string& getPerAcceptorParameterName

(

int

index

)

const

Get the name of a per-acceptor parameter.

Parameters:

index

the index of the parameter for which to get the name

Returns:

the parameter name

const std::string& getPerDonorParameterName

(

int

index

)

const

Get the name of a per-donor parameter.

Parameters:

index

the index of the parameter for which to get the name

Returns:

the parameter name

void setAcceptorParameters	(	int	index,
		int	a1,
		int	a2,
		int	a3,
		const std::vector< double > &	parameters
	)

Set the properties of an acceptor group.

Parameters:

	index	the index of the acceptor group to set
	a1	the index of the first particle for this acceptor group
	a2	the index of the second particle for this acceptor group. If the group only includes one particle, this must be -1.
	a3	the index of the third particle for this acceptor group. If the group includes less than three particles, this must be -1.
	parameters	the list of per-acceptor parameter values for the new acceptor

void setCutoffDistance

(

double

distance

)

Set the cutoff distance (in nm) being used.

All interactions for which the distance between d1 and a1 is greater than the cutoff will be ignored. If the NonbondedMethod in use is NoCutoff, this value will have no effect.

Parameters:

distance

the cutoff distance, measured in nm

void setDonorParameters	(	int	index,
		int	d1,
		int	d2,
		int	d3,
		const std::vector< double > &	parameters
	)

Set the properties of a donor group.

Parameters:

	index	the index of the donor group to set
	d1	the index of the first particle for this donor group
	d2	the index of the second particle for this donor group. If the group only includes one particle, this must be -1.
	d3	the index of the third particle for this donor group. If the group includes less than three particles, this must be -1.
	parameters	the list of per-donor parameter values for the new donor

void setEnergyFunction

(

const std::string &

energy

)

Set the algebraic expression that gives the interaction energy between a donor and an acceptor.

void setExclusionParticles	(	int	index,
		int	donor,
		int	acceptor
	)

Get the donor and acceptor in a pair whose interaction should be excluded.

Parameters:

	index	the index of the exclusion for which to get donor and acceptor indices
	particle1	the index of the donor
	particle2	the index of the acceptor

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 setPerAcceptorParameterName	(	int	index,
		const std::string &	name
	)

Set the name of a per-acceptor parameter.

Parameters:

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

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

Set the name of a per-donor parameter.

Parameters:

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

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

• CustomHbondForce.h