CustomAngleForce Class Reference

This class implements interactions between sets of three particles that depend on the angle between them. More...

Inheritance diagram for CustomAngleForce:

Public Member Functions
def	getNumAngles
	getNumAngles(CustomAngleForce self) -> int More...
def	getNumPerAngleParameters
	getNumPerAngleParameters(CustomAngleForce self) -> int More...
def	getNumGlobalParameters
	getNumGlobalParameters(CustomAngleForce self) -> int More...
def	getEnergyFunction
	getEnergyFunction(CustomAngleForce self) -> std::string const & More...
def	setEnergyFunction
	setEnergyFunction(CustomAngleForce self, std::string const & energy) More...
def	addPerAngleParameter
	addPerAngleParameter(CustomAngleForce self, std::string const & name) -> int More...
def	getPerAngleParameterName
	getPerAngleParameterName(CustomAngleForce self, int index) -> std::string const & More...
def	setPerAngleParameterName
	setPerAngleParameterName(CustomAngleForce self, int index, std::string const & name) More...
def	addGlobalParameter
	addGlobalParameter(CustomAngleForce self, std::string const & name, double defaultValue) -> int More...
def	getGlobalParameterName
	getGlobalParameterName(CustomAngleForce self, int index) -> std::string const & More...
def	setGlobalParameterName
	setGlobalParameterName(CustomAngleForce self, int index, std::string const & name) More...
def	getGlobalParameterDefaultValue
	getGlobalParameterDefaultValue(CustomAngleForce self, int index) -> double More...
def	setGlobalParameterDefaultValue
	setGlobalParameterDefaultValue(CustomAngleForce self, int index, double defaultValue) More...
def	addAngle
	addAngle(CustomAngleForce self, int particle1, int particle2, int particle3, vectord parameters) -> int More...
def	getAngleParameters
	getAngleParameters(CustomAngleForce self, int index) More...
def	setAngleParameters
	setAngleParameters(CustomAngleForce self, int index, int particle1, int particle2, int particle3, vectord parameters) More...
def	updateParametersInContext
	updateParametersInContext(CustomAngleForce self, Context context) More...
def	usesPeriodicBoundaryConditions
	usesPeriodicBoundaryConditions(CustomAngleForce self) -> bool More...
def	__init__
	init(OpenMM::CustomAngleForce self, std::string const & energy) -> CustomAngleForce init(OpenMM::CustomAngleForce self, CustomAngleForce other) -> CustomAngleForce More...
def	__del__
	del(OpenMM::CustomAngleForce self) More...
Public Member Functions inherited from Force
def	__init__
def	__del__
	del(OpenMM::Force self) More...
def	getForceGroup
	getForceGroup(Force self) -> int More...
def	setForceGroup
	setForceGroup(Force self, int group) More...
def	usesPeriodicBoundaryConditions
	usesPeriodicBoundaryConditions(Force self) -> bool More...
def	__copy__
def	__deepcopy__

Public Attributes
	this

Detailed Description

This class implements interactions between sets of three particles that depend on the angle between them.

Unlike HarmonicAngleForce, the functional form of the interaction is completely customizable, and may involve arbitrary algebraic expressions. In addition to the angle formed by the particles, it may depend on arbitrary global and per-angle parameters.

To use this class, create a CustomAngleForce object, passing an algebraic expression to the constructor that defines the interaction energy between each set of particles. The expression may depend on theta, the angle formed by the particles, as well as on any parameters you choose. Then call addPerAngleParameter() to define per-angle parameters, and addGlobalParameter() to define global parameters. The values of per-angle parameters are specified as part of the system definition, while values of global parameters may be modified during a simulation by calling Context::setParameter(). Finally, call addAngle() once for each angle. After an angle has been added, you can modify its parameters by calling setAngleParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

As an example, the following code creates a CustomAngleForce that implements a harmonic potential:

CustomAngleForce* force = new CustomAngleForce("0.5*k*(theta-theta0)^2");

This force depends on two parameters: the spring constant k and equilibrium angle theta0. The following code defines these parameters:

force->addPerAngleParameter("k");
force->addPerAngleParameter("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, floor, ceil, step, delta, select. 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. select(x,y,z) = z if x = 0, y otherwise.

Constructor & Destructor Documentation

def __init__	(		self,
			args
	)

init(OpenMM::CustomAngleForce self, std::string const & energy) -> CustomAngleForce init(OpenMM::CustomAngleForce self, CustomAngleForce other) -> CustomAngleForce

Create a CustomAngleForce.

Parameters

energy

an algebraic expression giving the interaction energy between three particles as a function of theta, the angle between them

References simtk.openmm.openmm.stripUnits().

def __del__

(

self

)

del(OpenMM::CustomAngleForce self)

References simtk.openmm.openmm.stripUnits().

Member Function Documentation

def addAngle	(		self,
			args
	)

addAngle(CustomAngleForce self, int particle1, int particle2, int particle3, vectord parameters) -> int

Add an angle term to the force field.

Parameters

particle1	the index of the first particle connected by the angle
particle2	the index of the second particle connected by the angle
particle3	the index of the third particle connected by the angle
parameters	the list of parameters for the new angle

References simtk.openmm.openmm.stripUnits().

def addGlobalParameter	(		self,
			args
	)

addGlobalParameter(CustomAngleForce self, std::string const & 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

References simtk.openmm.openmm.stripUnits().

def addPerAngleParameter	(		self,
			args
	)

addPerAngleParameter(CustomAngleForce self, std::string const & name) -> int

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

Parameters

name	the name of the parameter

References simtk.openmm.openmm.stripUnits().

def getAngleParameters	(		self,
			args
	)

getAngleParameters(CustomAngleForce self, int index)

Get the force field parameters for an angle term.

Parameters

index	the index of the angle for which to get parameters
particle1	the index of the first particle connected by the angle
particle2	the index of the second particle connected by the angle
particle3	the index of the third particle connected by the angle
parameters	the list of parameters for the angle

References simtk.openmm.openmm.stripUnits().

def getEnergyFunction	(		self,
			args
	)

getEnergyFunction(CustomAngleForce self) -> std::string const &

Get the algebraic expression that gives the interaction energy for each angle

References simtk.openmm.openmm.stripUnits().

def getGlobalParameterDefaultValue	(		self,
			args
	)

getGlobalParameterDefaultValue(CustomAngleForce 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

References simtk.openmm.openmm.stripUnits().

def getGlobalParameterName	(		self,
			args
	)

getGlobalParameterName(CustomAngleForce self, int index) -> std::string const &

Get the name of a global parameter.

Parameters

index

the index of the parameter for which to get the name

References simtk.openmm.openmm.stripUnits().

def getNumAngles	(		self,
			args
	)

getNumAngles(CustomAngleForce self) -> int

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

References simtk.openmm.openmm.stripUnits().

def getNumGlobalParameters	(		self,
			args
	)

getNumGlobalParameters(CustomAngleForce self) -> int

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

References simtk.openmm.openmm.stripUnits().

def getNumPerAngleParameters	(		self,
			args
	)

getNumPerAngleParameters(CustomAngleForce self) -> int

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

References simtk.openmm.openmm.stripUnits().

def getPerAngleParameterName	(		self,
			args
	)

getPerAngleParameterName(CustomAngleForce self, int index) -> std::string const &

Get the name of a per-angle parameter.

Parameters

index

the index of the parameter for which to get the name

References simtk.openmm.openmm.stripUnits().

def setAngleParameters	(		self,
			args
	)

setAngleParameters(CustomAngleForce self, int index, int particle1, int particle2, int particle3, vectord parameters)

Set the force field parameters for an angle term.

Parameters

index	the index of the angle for which to set parameters
particle1	the index of the first particle connected by the angle
particle2	the index of the second particle connected by the angle
particle3	the index of the third particle connected by the angle
parameters	the list of parameters for the angle

References simtk.openmm.openmm.stripUnits().

def setEnergyFunction	(		self,
			args
	)

setEnergyFunction(CustomAngleForce self, std::string const & energy)

Set the algebraic expression that gives the interaction energy for each angle

References simtk.openmm.openmm.stripUnits().

def setGlobalParameterDefaultValue	(		self,
			args
	)

setGlobalParameterDefaultValue(CustomAngleForce 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

References simtk.openmm.openmm.stripUnits().

def setGlobalParameterName	(		self,
			args
	)

setGlobalParameterName(CustomAngleForce self, int index, std::string const & 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

References simtk.openmm.openmm.stripUnits().

def setPerAngleParameterName	(		self,
			args
	)

setPerAngleParameterName(CustomAngleForce self, int index, std::string const & name)

Set the name of a per-angle parameter.

Parameters

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

References simtk.openmm.openmm.stripUnits().

def updateParametersInContext	(		self,
			args
	)

updateParametersInContext(CustomAngleForce self, Context context)

Update the per-angle 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 setAngleParameters() to modify this object's parameters, then call updateParametersInContext() to copy them over to the Context.

This method has several limitations. The only information it updates is the values of per-angle parameters. All other aspects of the Force (such as the energy function) are unaffected and can only be changed by reinitializing the Context. The set of particles involved in a angle cannot be changed, nor can new angles be added.

References simtk.openmm.openmm.stripUnits().

def usesPeriodicBoundaryConditions	(		self,
			args
	)

usesPeriodicBoundaryConditions(CustomAngleForce self) -> bool

Returns whether or not this force makes use of periodic boundary conditions.

References simtk.openmm.openmm.stripUnits().

Member Data Documentation

this

---

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

• openmm.py