This class implements the Amoeba multipole interaction. More...

Inheritance diagram for AmoebaMultipoleForce:

Public Member Functions
def	getNumMultipoles
	getNumMultipoles(AmoebaMultipoleForce self) -> int More...

def	getNonbondedMethod
	getNonbondedMethod(AmoebaMultipoleForce self) -> OpenMM::AmoebaMultipoleForce::NonbondedMethod More...

def	setNonbondedMethod
	setNonbondedMethod(AmoebaMultipoleForce self, OpenMM::AmoebaMultipoleForce::NonbondedMethod method) More...

def	getPolarizationType
	getPolarizationType(AmoebaMultipoleForce self) -> OpenMM::AmoebaMultipoleForce::PolarizationType More...

def	setPolarizationType
	setPolarizationType(AmoebaMultipoleForce self, OpenMM::AmoebaMultipoleForce::PolarizationType type) More...

def	getCutoffDistance
	getCutoffDistance(AmoebaMultipoleForce self) -> double More...

def	setCutoffDistance
	setCutoffDistance(AmoebaMultipoleForce self, double distance) More...

def	getAEwald
	getAEwald(AmoebaMultipoleForce self) -> double More...

def	setAEwald
	setAEwald(AmoebaMultipoleForce self, double aewald) More...

def	getPmeBSplineOrder
	getPmeBSplineOrder(AmoebaMultipoleForce self) -> int More...

def	getPmeGridDimensions
	getPmeGridDimensions(AmoebaMultipoleForce self) More...

def	setPmeGridDimensions
	setPmeGridDimensions(AmoebaMultipoleForce self, vectori gridDimension) More...

def	addMultipole
	addMultipole(AmoebaMultipoleForce self, double charge, vectord molecularDipole, vectord molecularQuadrupole, int axisType, int multipoleAtomZ, int multipoleAtomX, int multipoleAtomY, double thole, double dampingFactor, double polarity) -> int More...

def	getMultipoleParameters
	getMultipoleParameters(AmoebaMultipoleForce self, int index) More...

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

def	setCovalentMap
	setCovalentMap(AmoebaMultipoleForce self, int index, OpenMM::AmoebaMultipoleForce::CovalentType typeId, vectori covalentAtoms) More...

def	getCovalentMap
	getCovalentMap(AmoebaMultipoleForce self, int index, OpenMM::AmoebaMultipoleForce::CovalentType typeId) More...

def	getCovalentMaps
	getCovalentMaps(AmoebaMultipoleForce self, int index) More...

def	getMutualInducedMaxIterations
	getMutualInducedMaxIterations(AmoebaMultipoleForce self) -> int More...

def	setMutualInducedMaxIterations
	setMutualInducedMaxIterations(AmoebaMultipoleForce self, int inputMutualInducedMaxIterations) More...

def	getMutualInducedTargetEpsilon
	getMutualInducedTargetEpsilon(AmoebaMultipoleForce self) -> double More...

def	setMutualInducedTargetEpsilon
	setMutualInducedTargetEpsilon(AmoebaMultipoleForce self, double inputMutualInducedTargetEpsilon) More...

def	getEwaldErrorTolerance
	getEwaldErrorTolerance(AmoebaMultipoleForce self) -> double More...

def	setEwaldErrorTolerance
	setEwaldErrorTolerance(AmoebaMultipoleForce self, double tol) More...

def	getInducedDipoles
	getInducedDipoles(AmoebaMultipoleForce self, Context context) More...

def	getElectrostaticPotential
	getElectrostaticPotential(AmoebaMultipoleForce self, std::vector< Vec3,std::allocator< Vec3 > > const & inputGrid, Context context) More...

def	getSystemMultipoleMoments
	getSystemMultipoleMoments(AmoebaMultipoleForce self, Context context) More...

def	updateParametersInContext
	updateParametersInContext(AmoebaMultipoleForce self, Context context) More...

def	__init__
	init(OpenMM::AmoebaMultipoleForce self) -> AmoebaMultipoleForce init(OpenMM::AmoebaMultipoleForce self, AmoebaMultipoleForce other) -> AmoebaMultipoleForce More...

def	__del__
	del(OpenMM::AmoebaMultipoleForce 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

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

	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

Detailed Description

This class implements the Amoeba multipole interaction.

To use it, create an AmoebaMultipoleForce object then call addMultipole() once for each atom. After an entry has been added, you can modify its force field parameters by calling setMultipoleParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

Constructor & Destructor Documentation

def __init__	(	self,
		args
	)

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

Create an AmoebaMultipoleForce.

References simtk.openmm.openmm.stripUnits().

def __del__ ( self )

del(OpenMM::AmoebaMultipoleForce self)

References simtk.openmm.openmm.stripUnits().

Member Function Documentation

def addMultipole	(	self,
		args
	)

addMultipole(AmoebaMultipoleForce 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
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

References simtk.openmm.openmm.stripUnits().

def getAEwald ( self )

getAEwald(AmoebaMultipoleForce self) -> double

Get the Ewald alpha parameter. If this is 0 (the default), a value is chosen automatically based on the Ewald error tolerance.

References simtk.openmm.openmm.stripUnits().

def getCovalentMap	(	self,
		args
	)

getCovalentMap(AmoebaMultipoleForce self, int index, OpenMM::AmoebaMultipoleForce::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

References simtk.openmm.openmm.stripUnits().

def getCovalentMaps	(	self,
		args
	)

getCovalentMaps(AmoebaMultipoleForce 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

References simtk.openmm.openmm.stripUnits().

def getCutoffDistance ( self )

getCutoffDistance(AmoebaMultipoleForce 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.

References simtk.openmm.openmm.stripUnits().

def getElectrostaticPotential	(	self,
		args
	)

getElectrostaticPotential(AmoebaMultipoleForce self, std::vector< Vec3,std::allocator< Vec3 > > const & inputGrid, Context context)

Get the electrostatic potential.

Parameters

inputGrid	input grid points over which the potential is to be evaluated
context	context
outputElectrostaticPotential	output potential

References simtk.openmm.openmm.stripUnits().

def getEwaldErrorTolerance ( self )

getEwaldErrorTolerance(AmoebaMultipoleForce self) -> double

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 grid dimensions and separation (alpha) 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.

This can be overridden by explicitly setting an alpha parameter and grid dimensions to use.

References simtk.openmm.openmm.stripUnits().

def getInducedDipoles	(	self,
		args
	)

getInducedDipoles(AmoebaMultipoleForce self, Context context)

Get the induced dipole moments of all particles.

Parameters

context	the Context for which to get the induced dipoles
dipoles	the induced dipole moment of particle i is stored into the i'th element

References simtk.openmm.openmm.stripUnits().

def getMultipoleParameters	(	self,
		args
	)

getMultipoleParameters(AmoebaMultipoleForce 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
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

References simtk.openmm.openmm.stripUnits().

def getMutualInducedMaxIterations ( self )

getMutualInducedMaxIterations(AmoebaMultipoleForce self) -> int

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

References simtk.openmm.openmm.stripUnits().

def getMutualInducedTargetEpsilon ( self )

getMutualInducedTargetEpsilon(AmoebaMultipoleForce self) -> double

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

References simtk.openmm.openmm.stripUnits().

def getNonbondedMethod ( self )

getNonbondedMethod(AmoebaMultipoleForce self) -> OpenMM::AmoebaMultipoleForce::NonbondedMethod

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

References simtk.openmm.openmm.stripUnits().

def getNumMultipoles ( self )

getNumMultipoles(AmoebaMultipoleForce self) -> int

Get the number of particles in the potential function

References simtk.openmm.openmm.stripUnits().

def getPmeBSplineOrder ( self )

getPmeBSplineOrder(AmoebaMultipoleForce self) -> int

Get the B-spline order to use for PME charge spreading

References simtk.openmm.openmm.stripUnits().

def getPmeGridDimensions ( self )

getPmeGridDimensions(AmoebaMultipoleForce self)

Get the PME grid dimensions. If Ewald alpha is 0 (the default), this is ignored and grid dimensions are chosen automatically based on the Ewald error tolerance.

References simtk.openmm.openmm.stripUnits().

def getPolarizationType ( self )

getPolarizationType(AmoebaMultipoleForce self) -> OpenMM::AmoebaMultipoleForce::PolarizationType

Get polarization type

References simtk.openmm.openmm.stripUnits().

def getSystemMultipoleMoments	(	self,
		args
	)

getSystemMultipoleMoments(AmoebaMultipoleForce self, Context context)

Get the system multipole moments.

This method is most useful for non-periodic systems. When called for a periodic system, only the lowest nonvanishing moment has a well defined value. This means that if the system has a net nonzero charge, the dipole and quadrupole moments are not well defined and should be ignored. If the net charge is zero, the dipole moment is well defined (and really represents a dipole density), but the quadrupole moment is still undefined and should be ignored.

Parameters

context	context
outputMultipoleMonents	(charge, dipole_x, dipole_y, dipole_z, quadrupole_xx, quadrupole_xy, quadrupole_xz, quadrupole_yx, quadrupole_yy, quadrupole_yz, quadrupole_zx, quadrupole_zy, quadrupole_zz)

References simtk.openmm.openmm.stripUnits().

def setAEwald	(	self,
		args
	)

setAEwald(AmoebaMultipoleForce self, double aewald)

Set the Ewald alpha parameter. If this is 0 (the default), a value is chosen automatically based on the Ewald error tolerance.

Parameters

Ewald alpha parameter

References simtk.openmm.openmm.stripUnits().

def setCovalentMap	(	self,
		args
	)

setCovalentMap(AmoebaMultipoleForce self, int index, OpenMM::AmoebaMultipoleForce::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

References simtk.openmm.openmm.stripUnits().

def setCutoffDistance	(	self,
		args
	)

setCutoffDistance(AmoebaMultipoleForce 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

References simtk.openmm.openmm.stripUnits().

def setEwaldErrorTolerance	(	self,
		args
	)

setEwaldErrorTolerance(AmoebaMultipoleForce 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 grid dimensions and separation (alpha) 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.

This can be overridden by explicitly setting an alpha parameter and grid dimensions to use.

References simtk.openmm.openmm.stripUnits().

def setMultipoleParameters	(	self,
		args
	)

setMultipoleParameters(AmoebaMultipoleForce 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
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

References simtk.openmm.openmm.stripUnits().

def setMutualInducedMaxIterations	(	self,
		args
	)

setMutualInducedMaxIterations(AmoebaMultipoleForce self, int inputMutualInducedMaxIterations)

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

Parameters

max	number of iterations

References simtk.openmm.openmm.stripUnits().

def setMutualInducedTargetEpsilon	(	self,
		args
	)

setMutualInducedTargetEpsilon(AmoebaMultipoleForce 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

References simtk.openmm.openmm.stripUnits().

def setNonbondedMethod	(	self,
		args
	)

setNonbondedMethod(AmoebaMultipoleForce self, OpenMM::AmoebaMultipoleForce::NonbondedMethod method)

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

References simtk.openmm.openmm.stripUnits().

def setPmeGridDimensions	(	self,
		args
	)

setPmeGridDimensions(AmoebaMultipoleForce self, vectori gridDimension)

Set the PME grid dimensions. If Ewald alpha is 0 (the default), this is ignored and grid dimensions are chosen automatically based on the Ewald error tolerance.

Parameters

the	PME grid dimensions

References simtk.openmm.openmm.stripUnits().

def setPolarizationType	(	self,
		args
	)

setPolarizationType(AmoebaMultipoleForce self, OpenMM::AmoebaMultipoleForce::PolarizationType type)

Set the polarization type

References simtk.openmm.openmm.stripUnits().

def updateParametersInContext	(	self,
		args
	)

updateParametersInContext(AmoebaMultipoleForce self, Context context)

Update the multipole 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 setMultipoleParameters() to modify this object's parameters, then call updateParametersInState() to copy them over to the Context.

This method has several limitations. The only information it updates is the parameters of multipoles. All other aspects of the Force (the nonbonded method, the cutoff distance, etc.) are unaffected and can only be changed by reinitializing the Context. Furthermore, this method cannot be used to add new multipoles, only to change the parameters of existing ones.

References simtk.openmm.openmm.stripUnits().

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

this

Referenced by System.__init__().

ThreeFold = _openmm.AmoebaMultipoleForce_ThreeFold

static

ZBisect = _openmm.AmoebaMultipoleForce_ZBisect

static

ZOnly = _openmm.AmoebaMultipoleForce_ZOnly

static

ZThenX = _openmm.AmoebaMultipoleForce_ZThenX

static

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

openmm.py

Public Member Functions

Public Attributes

Static Public Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation