AmoebaTorsionTorsionForce Class Reference

This class implements the Amoeba torsion-torsion interaction. More...

Inheritance diagram for AmoebaTorsionTorsionForce:

Public Member Functions
def	getNumTorsionTorsions
	getNumTorsionTorsions(AmoebaTorsionTorsionForce self) -> int More...
def	getNumTorsionTorsionGrids
	getNumTorsionTorsionGrids(AmoebaTorsionTorsionForce self) -> int More...
def	addTorsionTorsion
	addTorsionTorsion(AmoebaTorsionTorsionForce self, int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex) -> int More...
def	getTorsionTorsionParameters
	getTorsionTorsionParameters(AmoebaTorsionTorsionForce self, int index) More...
def	setTorsionTorsionParameters
	setTorsionTorsionParameters(AmoebaTorsionTorsionForce self, int index, int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex) More...
def	getTorsionTorsionGrid
	getTorsionTorsionGrid(AmoebaTorsionTorsionForce self, int index) -> vectorddd More...
def	setTorsionTorsionGrid
	setTorsionTorsionGrid(AmoebaTorsionTorsionForce self, int index, vectorddd grid) More...
def	usesPeriodicBoundaryConditions
	usesPeriodicBoundaryConditions(AmoebaTorsionTorsionForce self) -> bool More...
def	__init__
	init(OpenMM::AmoebaTorsionTorsionForce self) -> AmoebaTorsionTorsionForce init(OpenMM::AmoebaTorsionTorsionForce self, AmoebaTorsionTorsionForce other) -> AmoebaTorsionTorsionForce More...
def	__del__
	del(OpenMM::AmoebaTorsionTorsionForce 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 torsion-torsion interaction.

To use it, create an AmoebaTorsionTorsionForce object then call addTorsionTorsion() once for each torsion-torsion. After a torsion-torsion has been added, you can modify its force field parameters by calling setTorsionTorsionParameters().

Constructor & Destructor Documentation

def __init__	(		self,
			args
	)

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

Create an AmoebaTorsionTorsionForce.

References simtk.openmm.openmm.stripUnits().

def __del__

(

self

)

del(OpenMM::AmoebaTorsionTorsionForce self)

References simtk.openmm.openmm.stripUnits().

Member Function Documentation

def addTorsionTorsion	(		self,
			args
	)

addTorsionTorsion(AmoebaTorsionTorsionForce self, int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex) -> int

Add a torsion-torsion term to the force field.

Parameters

particle1	the index of the first particle connected by the torsion-torsion
particle2	the index of the second particle connected by the torsion-torsion
particle3	the index of the third particle connected by the torsion-torsion
particle4	the index of the fourth particle connected by the torsion-torsion
particle5	the index of the fifth particle connected by the torsion-torsion
chiralCheckAtomIndex	the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check
gridIndex	the index to the grid to be used

References simtk.openmm.openmm.stripUnits().

def getNumTorsionTorsionGrids	(		self,
			args
	)

getNumTorsionTorsionGrids(AmoebaTorsionTorsionForce self) -> int

Get the number of torsion-torsion grids

References simtk.openmm.openmm.stripUnits().

def getNumTorsionTorsions	(		self,
			args
	)

getNumTorsionTorsions(AmoebaTorsionTorsionForce self) -> int

Get the number of torsion-torsion terms in the potential function

References simtk.openmm.openmm.stripUnits().

def getTorsionTorsionGrid	(		self,
			args
	)

getTorsionTorsionGrid(AmoebaTorsionTorsionForce self, int index) -> vectorddd

Get the torsion-torsion grid at the specified index

Parameters

gridIndex

the grid index

References simtk.openmm.openmm.stripUnits().

def getTorsionTorsionParameters	(		self,
			args
	)

getTorsionTorsionParameters(AmoebaTorsionTorsionForce self, int index)

Get the force field parameters for a torsion-torsion term.

Parameters

index	the index of the torsion-torsion for which to get parameters
particle1	the index of the first particle connected by the torsion-torsion
particle2	the index of the second particle connected by the torsion-torsion
particle3	the index of the third particle connected by the torsion-torsion
particle4	the index of the fourth particle connected by the torsion-torsion
particle5	the index of the fifth particle connected by the torsion-torsion
chiralCheckAtomIndex	the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check
gridIndex	the grid index

References simtk.openmm.openmm.stripUnits().

def setTorsionTorsionGrid	(		self,
			args
	)

setTorsionTorsionGrid(AmoebaTorsionTorsionForce self, int index, vectorddd grid)

Set the torsion-torsion grid at the specified index

Parameters

index	the index of the torsion-torsion for which to get parameters
grid	either 3 or 6 values may be specified per grid point. If the derivatives are omitted, they are calculated automatically by fitting a 2D spline to the energies. grid[x][y][0] = x value grid[x][y][1] = y value grid[x][y][2] = energy grid[x][y][3] = dEdx value grid[x][y][4] = dEdy value grid[x][y][5] = dEd(xy) value

References simtk.openmm.openmm.stripUnits().

def setTorsionTorsionParameters	(		self,
			args
	)

setTorsionTorsionParameters(AmoebaTorsionTorsionForce self, int index, int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex)

Set the force field parameters for a torsion-torsion term.

Parameters

index	the index of the torsion-torsion for which to set parameters
particle1	the index of the first particle connected by the torsion-torsion
particle2	the index of the second particle connected by the torsion-torsion
particle3	the index of the third particle connected by the torsion-torsion
particle4	the index of the fourth particle connected by the torsion-torsion
particle5	the index of the fifth particle connected by the torsion-torsion
chiralCheckAtomIndex	the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check
gridIndex	the grid index

References simtk.openmm.openmm.stripUnits().

def usesPeriodicBoundaryConditions	(		self,
			args
	)

usesPeriodicBoundaryConditions(AmoebaTorsionTorsionForce 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