AmoebaOutOfPlaneBendForce Class Reference

This class implements the Amoeba out-of-plane bend interaction. More...

Inheritance diagram for AmoebaOutOfPlaneBendForce:

Public Member Functions
def	getNumOutOfPlaneBends
	getNumOutOfPlaneBends(AmoebaOutOfPlaneBendForce self) -> int More...
def	setAmoebaGlobalOutOfPlaneBendCubic
	setAmoebaGlobalOutOfPlaneBendCubic(AmoebaOutOfPlaneBendForce self, double cubicK) More...
def	getAmoebaGlobalOutOfPlaneBendCubic
	getAmoebaGlobalOutOfPlaneBendCubic(AmoebaOutOfPlaneBendForce self) -> double More...
def	setAmoebaGlobalOutOfPlaneBendQuartic
	setAmoebaGlobalOutOfPlaneBendQuartic(AmoebaOutOfPlaneBendForce self, double quarticK) More...
def	getAmoebaGlobalOutOfPlaneBendQuartic
	getAmoebaGlobalOutOfPlaneBendQuartic(AmoebaOutOfPlaneBendForce self) -> double More...
def	setAmoebaGlobalOutOfPlaneBendPentic
	setAmoebaGlobalOutOfPlaneBendPentic(AmoebaOutOfPlaneBendForce self, double penticK) More...
def	getAmoebaGlobalOutOfPlaneBendPentic
	getAmoebaGlobalOutOfPlaneBendPentic(AmoebaOutOfPlaneBendForce self) -> double More...
def	setAmoebaGlobalOutOfPlaneBendSextic
	setAmoebaGlobalOutOfPlaneBendSextic(AmoebaOutOfPlaneBendForce self, double sexticK) More...
def	getAmoebaGlobalOutOfPlaneBendSextic
	getAmoebaGlobalOutOfPlaneBendSextic(AmoebaOutOfPlaneBendForce self) -> double More...
def	addOutOfPlaneBend
	addOutOfPlaneBend(AmoebaOutOfPlaneBendForce self, int particle1, int particle2, int particle3, int particle4, double k) -> int More...
def	getOutOfPlaneBendParameters
	getOutOfPlaneBendParameters(AmoebaOutOfPlaneBendForce self, int index) More...
def	setOutOfPlaneBendParameters
	setOutOfPlaneBendParameters(AmoebaOutOfPlaneBendForce self, int index, int particle1, int particle2, int particle3, int particle4, double k) More...
def	updateParametersInContext
	updateParametersInContext(AmoebaOutOfPlaneBendForce self, Context context) More...
def	usesPeriodicBoundaryConditions
	usesPeriodicBoundaryConditions(AmoebaOutOfPlaneBendForce self) -> bool More...
def	__init__
	init(OpenMM::AmoebaOutOfPlaneBendForce self) -> AmoebaOutOfPlaneBendForce init(OpenMM::AmoebaOutOfPlaneBendForce self, AmoebaOutOfPlaneBendForce other) -> AmoebaOutOfPlaneBendForce More...
def	__del__
	del(OpenMM::AmoebaOutOfPlaneBendForce 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 the Amoeba out-of-plane bend interaction.

To use it, create an OutOfPlaneBendForce object then call addOutOfPlaneBend() once for each outOfPlaneBend. After an out-of-plane bend has been added, you can modify its force field parameters by calling setOutOfPlaneBendParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

Constructor & Destructor Documentation

def __init__	(		self,
			args
	)

init(OpenMM::AmoebaOutOfPlaneBendForce self) -> AmoebaOutOfPlaneBendForce init(OpenMM::AmoebaOutOfPlaneBendForce self, AmoebaOutOfPlaneBendForce other) -> AmoebaOutOfPlaneBendForce

Create an AmoebaOutOfPlaneBendForce.

References simtk.openmm.openmm.stripUnits().

def __del__

(

self

)

del(OpenMM::AmoebaOutOfPlaneBendForce self)

References simtk.openmm.openmm.stripUnits().

Member Function Documentation

def addOutOfPlaneBend	(		self,
			args
	)

addOutOfPlaneBend(AmoebaOutOfPlaneBendForce self, int particle1, int particle2, int particle3, int particle4, double k) -> int

Add an out-of-plane bend term to the force field.

Parameters

particle1	the index of the first particle connected by the outOfPlaneBend
particle2	the index of the second particle connected by the outOfPlaneBend
particle3	the index of the third particle connected by the outOfPlaneBend
particle4	the index of the fourth particle connected by the outOfPlaneBend
k	the force constant for the out-of-plane bend

References simtk.openmm.openmm.stripUnits().

def getAmoebaGlobalOutOfPlaneBendCubic	(		self,
			args
	)

getAmoebaGlobalOutOfPlaneBendCubic(AmoebaOutOfPlaneBendForce self) -> double

Get the global cubic term

References simtk.openmm.openmm.stripUnits().

def getAmoebaGlobalOutOfPlaneBendPentic	(		self,
			args
	)

getAmoebaGlobalOutOfPlaneBendPentic(AmoebaOutOfPlaneBendForce self) -> double

Get the global pentic term

References simtk.openmm.openmm.stripUnits().

def getAmoebaGlobalOutOfPlaneBendQuartic	(		self,
			args
	)

getAmoebaGlobalOutOfPlaneBendQuartic(AmoebaOutOfPlaneBendForce self) -> double

Get the global quartic term

References simtk.openmm.openmm.stripUnits().

def getAmoebaGlobalOutOfPlaneBendSextic	(		self,
			args
	)

getAmoebaGlobalOutOfPlaneBendSextic(AmoebaOutOfPlaneBendForce self) -> double

Get the global sextic term

References simtk.openmm.openmm.stripUnits().

def getNumOutOfPlaneBends	(		self,
			args
	)

getNumOutOfPlaneBends(AmoebaOutOfPlaneBendForce self) -> int

Get the number of out-of-plane bend terms in the potential function

References simtk.openmm.openmm.stripUnits().

def getOutOfPlaneBendParameters	(		self,
			args
	)

getOutOfPlaneBendParameters(AmoebaOutOfPlaneBendForce self, int index)

Get the force field parameters for an out-of-plane bend term.

Parameters

index	the index of the outOfPlaneBend for which to get parameters
particle1	the index of the first particle connected by the outOfPlaneBend
particle2	the index of the second particle connected by the outOfPlaneBend
particle3	the index of the third particle connected by the outOfPlaneBend
particle4	the index of the fourth particle connected by the outOfPlaneBend
k	the force constant for the out-of-plane bend

References simtk.openmm.openmm.stripUnits().

def setAmoebaGlobalOutOfPlaneBendCubic	(		self,
			args
	)

setAmoebaGlobalOutOfPlaneBendCubic(AmoebaOutOfPlaneBendForce self, double cubicK)

Set the global cubic term

Parameters

cubicK

the cubic force constant for the angle

References simtk.openmm.openmm.stripUnits().

def setAmoebaGlobalOutOfPlaneBendPentic	(		self,
			args
	)

setAmoebaGlobalOutOfPlaneBendPentic(AmoebaOutOfPlaneBendForce self, double penticK)

Set the global pentic term

Parameters

penticK

the pentic force constant for the angle

References simtk.openmm.openmm.stripUnits().

def setAmoebaGlobalOutOfPlaneBendQuartic	(		self,
			args
	)

setAmoebaGlobalOutOfPlaneBendQuartic(AmoebaOutOfPlaneBendForce self, double quarticK)

Set the global cubic term

Parameters

quarticK

the quartic force constant for the angle

References simtk.openmm.openmm.stripUnits().

def setAmoebaGlobalOutOfPlaneBendSextic	(		self,
			args
	)

setAmoebaGlobalOutOfPlaneBendSextic(AmoebaOutOfPlaneBendForce self, double sexticK)

Set the global sextic term

Parameters

sexticK

the sextic force constant for the angle

References simtk.openmm.openmm.stripUnits().

def setOutOfPlaneBendParameters	(		self,
			args
	)

setOutOfPlaneBendParameters(AmoebaOutOfPlaneBendForce self, int index, int particle1, int particle2, int particle3, int particle4, double k)

Set the force field parameters for an out-of-plane bend term.

Parameters

index	the index of the outOfPlaneBend for which to set parameters
particle1	the index of the first particle connected by the outOfPlaneBend
particle2	the index of the second particle connected by the outOfPlaneBend
particle3	the index of the third particle connected by the outOfPlaneBend
particle4	the index of the fourth particle connected by the outOfPlaneBend
k	the force constant for the out-of-plane bend

References simtk.openmm.openmm.stripUnits().

def updateParametersInContext	(		self,
			args
	)

updateParametersInContext(AmoebaOutOfPlaneBendForce self, Context context)

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

The only information this method updates is the values of per-bend term parameters. The set of particles involved in a term cannot be changed, nor can new terms be added.

References simtk.openmm.openmm.stripUnits().

def usesPeriodicBoundaryConditions	(		self,
			args
	)

usesPeriodicBoundaryConditions(AmoebaOutOfPlaneBendForce self) -> bool

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

References simtk.openmm.openmm.stripUnits().

Member Data Documentation

this

Referenced by System.__init__().

---

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

• openmm.py