AmoebaStretchBendForce Class Reference

This class implements the Amoeba stretch-bend interaction. More...

Inheritance diagram for AmoebaStretchBendForce:

Public Member Functions
def	getNumStretchBends
	getNumStretchBends(AmoebaStretchBendForce self) -> int More...
def	addStretchBend
	addStretchBend(AmoebaStretchBendForce self, int particle1, int particle2, int particle3, double lengthAB, double lengthCB, double angle, double k) -> int More...
def	getStretchBendParameters
	getStretchBendParameters(AmoebaStretchBendForce self, int index) More...
def	setStretchBendParameters
	setStretchBendParameters(AmoebaStretchBendForce self, int index, int particle1, int particle2, int particle3, double lengthAB, double lengthCB, double angle, double k) More...
def	updateParametersInContext
	updateParametersInContext(AmoebaStretchBendForce self, Context context) More...
def	__init__
	init(OpenMM::AmoebaStretchBendForce self) -> AmoebaStretchBendForce init(OpenMM::AmoebaStretchBendForce self, AmoebaStretchBendForce other) -> AmoebaStretchBendForce More...
def	__del__
	del(OpenMM::AmoebaStretchBendForce 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	__copy__
def	__deepcopy__

Public Attributes
	this

Detailed Description

This class implements the Amoeba stretch-bend interaction.

To use it, create a StretchBendForce object then call addStretchBend() once for each stretch-bend. After a stretch-bend has been added, you can modify its force field parameters by calling setStretchBendParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

Constructor & Destructor Documentation

def __init__	(		self,
			args
	)

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

Create an AmoebaStretchBendForce.

References simtk.openmm.openmm.stripUnits().

def __del__

(

self

)

del(OpenMM::AmoebaStretchBendForce self)

References simtk.openmm.openmm.stripUnits().

Member Function Documentation

def addStretchBend	(		self,
			args
	)

addStretchBend(AmoebaStretchBendForce self, int particle1, int particle2, int particle3, double lengthAB, double lengthCB, double angle, double k) -> int

Add a stretch-bend term to the force field.

Parameters

particle1	the index of the first particle connected by the stretch-bend
particle2	the index of the second particle connected by the stretch-bend
particle3	the index of the third particle connected by the stretch-bend
lengthAB	the equilibrium length of the stretch-bend in bond ab [particle1, particle2], measured in nm
lengthCB	the equilibrium length of the stretch-bend in bond cb [particle3, particle2], measured in nm
angle	the equilibrium angle in radians
k	the force constant for the stretch-bend

References simtk.openmm.openmm.stripUnits().

def getNumStretchBends

(

self

)

getNumStretchBends(AmoebaStretchBendForce self) -> int

Get the number of stretch-bend terms in the potential function

References simtk.openmm.openmm.stripUnits().

def getStretchBendParameters	(		self,
			args
	)

getStretchBendParameters(AmoebaStretchBendForce self, int index)

Get the force field parameters for a stretch-bend term.

Parameters

index	the index of the stretch-bend for which to get parameters
particle1	the index of the first particle connected by the stretch-bend
particle2	the index of the second particle connected by the stretch-bend
particle3	the index of the third particle connected by the stretch-bend
lengthAB	the equilibrium length of the stretch-bend in bond ab [particle1, particle2], measured in nm
lengthCB	the equilibrium length of the stretch-bend in bond cb [particle3, particle2], measured in nm
angle	the equilibrium angle in radians
k	the force constant for the stretch-bend

References simtk.openmm.openmm.stripUnits().

def setStretchBendParameters	(		self,
			args
	)

setStretchBendParameters(AmoebaStretchBendForce self, int index, int particle1, int particle2, int particle3, double lengthAB, double lengthCB, double angle, double k)

Set the force field parameters for a stretch-bend term.

Parameters

index	the index of the stretch-bend for which to set parameters
particle1	the index of the first particle connected by the stretch-bend
particle2	the index of the second particle connected by the stretch-bend
particle3	the index of the third particle connected by the stretch-bend
lengthAB	the equilibrium length of the stretch-bend in bond ab [particle1, particle2], measured in nm
lengthCB	the equilibrium length of the stretch-bend in bond cb [particle3, particle2], measured in nm
angle	the equilibrium angle in radians
k	the force constant for the stretch-bend

References simtk.openmm.openmm.stripUnits().

def updateParametersInContext	(		self,
			args
	)

updateParametersInContext(AmoebaStretchBendForce self, Context context)

Update the per-stretch-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 setStretchBendParameters() to modify this object's parameters, then call updateParametersInState() to copy them over to the Context.

The only information this method updates is the values of per-stretch-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().

Member Data Documentation

this

Referenced by System.__init__().

---

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

• openmm.py