CustomNonbondedForce Class Reference

This class implements nonbonded interactions between particles. More...

Inheritance diagram for CustomNonbondedForce:

List of all members.

Public Member Functions
def	getNumParticles
	getNumParticles(self) -> int
def	getNumExclusions
	getNumExclusions(self) -> int
def	getNumPerParticleParameters
	getNumPerParticleParameters(self) -> int
def	getNumGlobalParameters
	getNumGlobalParameters(self) -> int
def	getNumFunctions
	getNumFunctions(self) -> int
def	getEnergyFunction
	getEnergyFunction(self) -> string
def	setEnergyFunction
	setEnergyFunction(self, string energy)
def	getNonbondedMethod
	getNonbondedMethod(self) -> NonbondedMethod
def	setNonbondedMethod
	setNonbondedMethod(self, NonbondedMethod method)
def	getCutoffDistance
	getCutoffDistance(self) -> double
def	setCutoffDistance
	setCutoffDistance(self, double distance)
def	addPerParticleParameter
	addPerParticleParameter(self, string name) -> int
def	getPerParticleParameterName
	getPerParticleParameterName(self, int index) -> string
def	setPerParticleParameterName
	setPerParticleParameterName(self, int index, string name)
def	addGlobalParameter
	addGlobalParameter(self, string name, double defaultValue) -> int
def	getGlobalParameterName
	getGlobalParameterName(self, int index) -> string
def	setGlobalParameterName
	setGlobalParameterName(self, int index, string name)
def	getGlobalParameterDefaultValue
	getGlobalParameterDefaultValue(self, int index) -> double
def	setGlobalParameterDefaultValue
	setGlobalParameterDefaultValue(self, int index, double defaultValue)
def	addParticle
	addParticle(self, vectord parameters) -> int
def	getParticleParameters
	getParticleParameters(self, int index)
def	setParticleParameters
	setParticleParameters(self, int index, vectord parameters)
def	addExclusion
	addExclusion(self, int particle1, int particle2) -> int
def	getExclusionParticles
	getExclusionParticles(self, int index)
def	setExclusionParticles
	setExclusionParticles(self, int index, int particle1, int particle2)
def	addFunction
	addFunction(self, string name, vectord values, double min, double max) -> int
def	getFunctionParameters
	getFunctionParameters(self, int index)
def	setFunctionParameters
	setFunctionParameters(self, int index, string name, vectord values, double min, double max)
def	__init__
	__init__(self, string energy) -> CustomNonbondedForce __init__(self, CustomNonbondedForce other) -> CustomNonbondedForce
def	__del__
	__del__(self)
Public Attributes
	this
Static Public Attributes
	NoCutoff = _openmm.CustomNonbondedForce_NoCutoff
	CutoffNonPeriodic = _openmm.CustomNonbondedForce_CutoffNonPeriodic
	CutoffPeriodic = _openmm.CustomNonbondedForce_CutoffPeriodic

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Detailed Description

This class implements nonbonded interactions between particles.

Unlike NonbondedForce, the functional form of the interaction is completely customizable, and may involve arbitrary algebraic expressions and tabulated functions. It may depend on the distance between particles, as well as on arbitrary global and per-particle parameters. It also optionally supports periodic boundary conditions and cutoffs for long range interactions.

To use this class, create a CustomNonbondedForce object, passing an algebraic expression to the constructor that defines the interaction energy between each pair of particles. The expression may depend on r, the distance between the particles, as well as on any parameters you choose. Then call addPerParticleParameter() to define per-particle parameters, and addGlobalParameter() to define global parameters. The values of per-particle 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 addParticle() once for each particle in the System to set the values of its per-particle parameters. 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().

CustomNonbondedForce also lets you specify "exclusions", particular pairs of particles 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 CustomNonbondedForce that implements a 12-6 Lennard-Jones potential:

CustomNonbondedForce* force = new CustomNonbondedForce("4*epsilon*((sigma/r)^12-(sigma/r)^6); sigma=0.5*(sigma1*sigma2); epsilon=sqrt(epsilon1*epsilon2)");

This force depends on two parameters: sigma and epsilon. The following code defines these as per-particle parameters:

     force->addPerParticleParameter("sigma");
     force->addPerParticleParameter("epsilon");
     

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. The names of per-particle parameters have the suffix "1" or "2" appended to them to indicate the values for the two interacting particles. As seen in the above example, the 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 the expression.

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Member Function Documentation

def __del__

(

self

)

__del__(self)

Reimplemented from Force.

def __init__	(		self,
			args
	)

__init__(self, string energy) -> CustomNonbondedForce __init__(self, CustomNonbondedForce other) -> CustomNonbondedForce

Create a CustomNonbondedForce.

Parameters:

energy

an algebraic expression giving the interaction energy between two particles as a function of r, the distance between them, as well as any global and per-particle parameters

def addExclusion	(		self,
			args
	)

addExclusion(self, int particle1, int particle2) -> int

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

def addFunction	(		self,
			args
	)

addFunction(self, string name, vectord values, double min, double max) -> int

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

def addGlobalParameter	(		self,
			args
	)

addGlobalParameter(self, string name, double defaultValue) -> int

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

def addParticle	(		self,
			args
	)

addParticle(self, vectord parameters) -> int

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

def addPerParticleParameter	(		self,
			args
	)

addPerParticleParameter(self, string name) -> int

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

Parameters:

name

the name of the parameter

def getCutoffDistance

(

self

)

getCutoffDistance(self) -> double

Get the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use is NoCutoff, this value will have no effect.

def getEnergyFunction

(

self

)

getEnergyFunction(self) -> string

Get the algebraic expression that gives the interaction energy between two particles

def getExclusionParticles	(		self,
			args
	)

getExclusionParticles(self, int index)

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

def getFunctionParameters	(		self,
			args
	)

getFunctionParameters(self, int index)

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

def getGlobalParameterDefaultValue	(		self,
			args
	)

getGlobalParameterDefaultValue(self, int index) -> double

Get the default value of a global parameter.

Parameters:

index

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

def getGlobalParameterName	(		self,
			args
	)

getGlobalParameterName(self, int index) -> string

Get the name of a global parameter.

Parameters:

index

the index of the parameter for which to get the name

def getNonbondedMethod

(

self

)

getNonbondedMethod(self) -> NonbondedMethod

Get the method used for handling long range nonbonded interactions.

def getNumExclusions

(

self

)

getNumExclusions(self) -> int

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

def getNumFunctions

(

self

)

getNumFunctions(self) -> int

Get the number of tabulated functions that have been defined.

def getNumGlobalParameters

(

self

)

getNumGlobalParameters(self) -> int

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

def getNumParticles

(

self

)

getNumParticles(self) -> int

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

def getNumPerParticleParameters

(

self

)

getNumPerParticleParameters(self) -> int

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

def getParticleParameters	(		self,
			args
	)

getParticleParameters(self, int index)

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

def getPerParticleParameterName	(		self,
			args
	)

getPerParticleParameterName(self, int index) -> string

Get the name of a per-particle parameter.

Parameters:

index

the index of the parameter for which to get the name

def setCutoffDistance	(		self,
			args
	)

setCutoffDistance(self, 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

def setEnergyFunction	(		self,
			args
	)

setEnergyFunction(self, string energy)

Set the algebraic expression that gives the interaction energy between two particles

def setExclusionParticles	(		self,
			args
	)

setExclusionParticles(self, 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

def setFunctionParameters	(		self,
			args
	)

setFunctionParameters(self, int index, string name, vectord 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

def setGlobalParameterDefaultValue	(		self,
			args
	)

setGlobalParameterDefaultValue(self, 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

def setGlobalParameterName	(		self,
			args
	)

setGlobalParameterName(self, int index, 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

def setNonbondedMethod	(		self,
			args
	)

setNonbondedMethod(self, NonbondedMethod method)

Set the method used for handling long range nonbonded interactions.

def setParticleParameters	(		self,
			args
	)

setParticleParameters(self, int index, vectord 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

def setPerParticleParameterName	(		self,
			args
	)

setPerParticleParameterName(self, int index, 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

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Member Data Documentation

CutoffNonPeriodic = _openmm.CustomNonbondedForce_CutoffNonPeriodic [static]

CutoffPeriodic = _openmm.CustomNonbondedForce_CutoffPeriodic [static]

NoCutoff = _openmm.CustomNonbondedForce_NoCutoff [static]

this

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

• openmm.py