AmoebaMultipoleForce Class Reference

This class implements the Amoeba multipole interaction To use it, create a MultipoleForce object then call addMultipole() once for each atom. More...

Inheritance diagram for AmoebaMultipoleForce:

List of all members.

Public Member Functions
def	getNumMultipoles
	getNumMultipoles(self) -> int
def	getNonbondedMethod
	getNonbondedMethod(self) -> AmoebaNonbondedMethod
def	setNonbondedMethod
	setNonbondedMethod(self, AmoebaNonbondedMethod method)
def	getPolarizationType
	getPolarizationType(self) -> AmoebaPolarizationType
def	setPolarizationType
	setPolarizationType(self, AmoebaPolarizationType type)
def	getCutoffDistance
	getCutoffDistance(self) -> double
def	setCutoffDistance
	setCutoffDistance(self, double distance)
def	getAEwald
	getAEwald(self) -> double
def	setAEwald
	setAEwald(self, double aewald)
def	getPmeBSplineOrder
	getPmeBSplineOrder(self) -> int
def	getPmeGridDimensions
	getPmeGridDimensions(self)
def	setPmeGridDimensions
	setPmeGridDimensions(self, vectori gridDimension)
def	addParticle
	addParticle(self, double charge, vectord molecularDipole, vectord molecularQuadrupole, int axisType, int multipoleAtomZ, int multipoleAtomX, int multipoleAtomY, double thole, double dampingFactor, double polarity) -> int
def	getMultipoleParameters
	getMultipoleParameters(self, int index)
def	setMultipoleParameters
	setMultipoleParameters(self, int index, double charge, vectord molecularDipole, vectord molecularQuadrupole, int axisType, int multipoleAtomZ, int multipoleAtomX, int multipoleAtomY, double thole, double dampingFactor, double polarity)
def	setCovalentMap
	setCovalentMap(self, int index, CovalentType typeId, vectori covalentAtoms)
def	getCovalentMap
	getCovalentMap(self, int index, CovalentType typeId)
def	getCovalentMaps
	getCovalentMaps(self, int index)
def	getMutualInducedMaxIterations
	getMutualInducedMaxIterations(self) -> int
def	setMutualInducedMaxIterations
	setMutualInducedMaxIterations(self, int inputMutualInducedMaxIterations)
def	getMutualInducedTargetEpsilon
	getMutualInducedTargetEpsilon(self) -> double
def	setMutualInducedTargetEpsilon
	setMutualInducedTargetEpsilon(self, double inputMutualInducedTargetEpsilon)
def	getEwaldErrorTolerance
	getEwaldErrorTolerance(self) -> double
def	setEwaldErrorTolerance
	setEwaldErrorTolerance(self, double tol)
def	__init__
	__init__(self) -> AmoebaMultipoleForce __init__(self, AmoebaMultipoleForce other) -> AmoebaMultipoleForce
def	__del__
	__del__(self)
Public Attributes
	this
Static Public Attributes
	NoCutoff = _openmm.AmoebaMultipoleForce_NoCutoff
	PME = _openmm.AmoebaMultipoleForce_PME
	Mutual = _openmm.AmoebaMultipoleForce_Mutual
	Direct = _openmm.AmoebaMultipoleForce_Direct
	ZThenX = _openmm.AmoebaMultipoleForce_ZThenX
	Bisector = _openmm.AmoebaMultipoleForce_Bisector
	ZBisect = _openmm.AmoebaMultipoleForce_ZBisect
	ThreeFold = _openmm.AmoebaMultipoleForce_ThreeFold
	ZOnly = _openmm.AmoebaMultipoleForce_ZOnly
	NoAxisType = _openmm.AmoebaMultipoleForce_NoAxisType
	LastAxisTypeIndex = _openmm.AmoebaMultipoleForce_LastAxisTypeIndex
	SOR = _openmm.AmoebaMultipoleForce_SOR
	Covalent12 = _openmm.AmoebaMultipoleForce_Covalent12
	Covalent13 = _openmm.AmoebaMultipoleForce_Covalent13
	Covalent14 = _openmm.AmoebaMultipoleForce_Covalent14
	Covalent15 = _openmm.AmoebaMultipoleForce_Covalent15
	PolarizationCovalent11 = _openmm.AmoebaMultipoleForce_PolarizationCovalent11
	PolarizationCovalent12 = _openmm.AmoebaMultipoleForce_PolarizationCovalent12
	PolarizationCovalent13 = _openmm.AmoebaMultipoleForce_PolarizationCovalent13
	PolarizationCovalent14 = _openmm.AmoebaMultipoleForce_PolarizationCovalent14
	CovalentEnd = _openmm.AmoebaMultipoleForce_CovalentEnd

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Detailed Description

This class implements the Amoeba multipole interaction To use it, create a MultipoleForce object then call addMultipole() once for each atom.

After a entry has been added, you can modify its force field parameters by calling setMultipoleParameters().

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Member Function Documentation

def __del__

(

self

)

__del__(self)

Reimplemented from Force.

def __init__	(		self,
			args
	)

__init__(self) -> AmoebaMultipoleForce __init__(self, AmoebaMultipoleForce other) -> AmoebaMultipoleForce

Create a Amoeba MultipoleForce.

def addParticle	(		self,
			args
	)

addParticle(self, double charge, vectord molecularDipole, vectord molecularQuadrupole, int axisType, int multipoleAtomZ, int multipoleAtomX, int multipoleAtomY, double thole, double dampingFactor, double polarity) -> int

Add multipole-related info for a particle

Parameters:

	charge	the particle's charge
	molecularDipole	the particle's molecular dipole (vector of size 3)
	molecularQuadrupole	the particle's molecular quadrupole (vector of size 9)
	axisType	the particle's axis type ( ZThenX, Bisector )
	multipoleAtomZ	index of first atom used in constructing lab<->molecular frames
	multipoleAtomX	index of second atom used in constructing lab<->molecular frames
	multipoleAtomY	index of second atom used in constructing lab<->molecular frames
	thole	Thole parameter
	dampingFactor	dampingFactor parameter
	polarity	polarity parameter

def getAEwald

(

self

)

getAEwald(self) -> double

Get the aEwald parameter

def getCovalentMap	(		self,
			args
	)

getCovalentMap(self, int index, CovalentType typeId)

Get the CovalentMap for an atom

Parameters:

	index	the index of the atom for which to set parameters
	typeId	CovalentTypes type
	covalentAtoms	output vector of covalent atoms associated w/ the specfied CovalentType

def getCovalentMaps	(		self,
			args
	)

getCovalentMaps(self, int index)

Get the CovalentMap for an atom

Parameters:

	index	the index of the atom for which to set parameters
	covalentLists	output vector of covalent lists of atoms

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 getEwaldErrorTolerance

(

self

)

getEwaldErrorTolerance(self) -> double

Get the scaling distance cutoff (nm)

Parameters:

	scaling	distance cutoff Get the electric constant
	the	electric constant Get the error tolerance for Ewald summation. This corresponds to the fractional error in the forces which is acceptable. This value is used to select the reciprocal space cutoff and separation parameter so that the average error level will be less than the tolerance. There is not a rigorous guarantee that all forces on all atoms will be less than the tolerance, however.

def getMultipoleParameters	(		self,
			args
	)

getMultipoleParameters(self, int index)

Get the multipole parameters for a particle.

Parameters:

	index	the index of the atom for which to get parameters
	charge	the particle's charge
	molecularDipole	the particle's molecular dipole (vector of size 3)
	molecularQuadrupole	the particle's molecular quadrupole (vector of size 9)
	axisType	the particle's axis type ( ZThenX, Bisector )
	multipoleAtomZ	index of first atom used in constructing lab<->molecular frames
	multipoleAtomX	index of second atom used in constructing lab<->molecular frames
	multipoleAtomY	index of second atom used in constructing lab<->molecular frames
	thole	Thole parameter
	dampingFactor	dampingFactor parameter
	polarity	polarity parameter

def getMutualInducedMaxIterations

(

self

)

getMutualInducedMaxIterations(self) -> int

Get the iteration method to be used for calculating the mutual induced dipoles

Parameters:

iteration

method to be used for calculating the mutual induced dipole Get the max number of iterations to be used in calculating the mutual induced dipoles

def getMutualInducedTargetEpsilon

(

self

)

getMutualInducedTargetEpsilon(self) -> double

Get the target epsilon to be used to test for convergence of iterative method used in calculating the mutual induced dipoles

def getNonbondedMethod

(

self

)

getNonbondedMethod(self) -> AmoebaNonbondedMethod

Get the method used for handling long-range nonbonded interactions.

def getNumMultipoles

(

self

)

getNumMultipoles(self) -> int

Get the number of particles in the potential function

def getPmeBSplineOrder

(

self

)

getPmeBSplineOrder(self) -> int

Get the B-spline order parameter

def getPmeGridDimensions

(

self

)

getPmeGridDimensions(self)

Set the B-spline order parameter

Parameters:

the

B-spline order parameter Get the PME grid dimensions

def getPolarizationType

(

self

)

getPolarizationType(self) -> AmoebaPolarizationType

Get polarization type

def setAEwald	(		self,
			args
	)

setAEwald(self, double aewald)

Set the aEwald parameter

Parameters:

Ewald

parameter

def setCovalentMap	(		self,
			args
	)

setCovalentMap(self, int index, CovalentType typeId, vectori covalentAtoms)

Set the CovalentMap for an atom

Parameters:

	index	the index of the atom for which to set parameters
	typeId	CovalentTypes type
	covalentAtoms	vector of covalent atoms associated w/ the specfied CovalentType

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 setEwaldErrorTolerance	(		self,
			args
	)

setEwaldErrorTolerance(self, double tol)

Get the error tolerance for Ewald summation. This corresponds to the fractional error in the forces which is acceptable. This value is used to select the reciprocal space cutoff and separation parameter so that the average error level will be less than the tolerance. There is not a rigorous guarantee that all forces on all atoms will be less than the tolerance, however.

def setMultipoleParameters	(		self,
			args
	)

setMultipoleParameters(self, int index, double charge, vectord molecularDipole, vectord molecularQuadrupole, int axisType, int multipoleAtomZ, int multipoleAtomX, int multipoleAtomY, double thole, double dampingFactor, double polarity)

Set the multipole parameters for a particle.

Parameters:

	index	the index of the atom for which to set parameters
	charge	the particle's charge
	molecularDipole	the particle's molecular dipole (vector of size 3)
	molecularQuadrupole	the particle's molecular quadrupole (vector of size 9)
	axisType	the particle's axis type ( ZThenX, Bisector )
	multipoleAtomZ	index of first atom used in constructing lab<->molecular frames
	multipoleAtomX	index of second atom used in constructing lab<->molecular frames
	multipoleAtomY	index of second atom used in constructing lab<->molecular frames
	polarity	polarity parameter

def setMutualInducedMaxIterations	(		self,
			args
	)

setMutualInducedMaxIterations(self, int inputMutualInducedMaxIterations)

Set the max number of iterations to be used in calculating the mutual induced dipoles

Parameters:

max

number of iterations

def setMutualInducedTargetEpsilon	(		self,
			args
	)

setMutualInducedTargetEpsilon(self, double inputMutualInducedTargetEpsilon)

Set the target epsilon to be used to test for convergence of iterative method used in calculating the mutual induced dipoles

Parameters:

target

epsilon

def setNonbondedMethod	(		self,
			args
	)

setNonbondedMethod(self, AmoebaNonbondedMethod method)

Set the method used for handling long-range nonbonded interactions.

def setPmeGridDimensions	(		self,
			args
	)

setPmeGridDimensions(self, vectori gridDimension)

Set the PME grid dimensions

Parameters:

the

PME grid dimensions

def setPolarizationType	(		self,
			args
	)

setPolarizationType(self, AmoebaPolarizationType type)

Set the polarization type

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Member Data Documentation

Bisector = _openmm.AmoebaMultipoleForce_Bisector [static]

Covalent12 = _openmm.AmoebaMultipoleForce_Covalent12 [static]

Covalent13 = _openmm.AmoebaMultipoleForce_Covalent13 [static]

Covalent14 = _openmm.AmoebaMultipoleForce_Covalent14 [static]

Covalent15 = _openmm.AmoebaMultipoleForce_Covalent15 [static]

CovalentEnd = _openmm.AmoebaMultipoleForce_CovalentEnd [static]

Direct = _openmm.AmoebaMultipoleForce_Direct [static]

LastAxisTypeIndex = _openmm.AmoebaMultipoleForce_LastAxisTypeIndex [static]

Mutual = _openmm.AmoebaMultipoleForce_Mutual [static]

NoAxisType = _openmm.AmoebaMultipoleForce_NoAxisType [static]

NoCutoff = _openmm.AmoebaMultipoleForce_NoCutoff [static]

PME = _openmm.AmoebaMultipoleForce_PME [static]

PolarizationCovalent11 = _openmm.AmoebaMultipoleForce_PolarizationCovalent11 [static]

PolarizationCovalent12 = _openmm.AmoebaMultipoleForce_PolarizationCovalent12 [static]

PolarizationCovalent13 = _openmm.AmoebaMultipoleForce_PolarizationCovalent13 [static]

PolarizationCovalent14 = _openmm.AmoebaMultipoleForce_PolarizationCovalent14 [static]

SOR = _openmm.AmoebaMultipoleForce_SOR [static]

this

ThreeFold = _openmm.AmoebaMultipoleForce_ThreeFold [static]

ZBisect = _openmm.AmoebaMultipoleForce_ZBisect [static]

ZOnly = _openmm.AmoebaMultipoleForce_ZOnly [static]

ZThenX = _openmm.AmoebaMultipoleForce_ZThenX [static]

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

• openmm.py