AmoebaMultipoleForce¶

class simtk.openmm.openmm.AmoebaMultipoleForce(*args)¶

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().

__init__(self) → AmoebaMultipoleForce¶

__init__(self, other) -> AmoebaMultipoleForce

Create an AmoebaMultipoleForce.

Methods

`__init__`((self) -> AmoebaMultipoleForce)	__init__(self, other) -> AmoebaMultipoleForce
`addMultipole`((self, charge, molecularDipole, ...)	Add multipole-related info for a particle
`getAEwald`((self) -> double)	Get the Ewald alpha parameter.
`getCovalentMap`(self, index, typeId)	Get the CovalentMap for an atom
`getCovalentMaps`(self, index)	Get the CovalentMap for an atom
`getCutoffDistance`((self) -> double)	Get the cutoff distance (in nm) being used for nonbonded interactions.
`getElectrostaticPotential`(self, inputGrid, ...)	Get the electrostatic potential.
`getEwaldErrorTolerance`((self) -> double)	Get the error tolerance for Ewald summation.
`getExtrapolationCoefficients`((self) -> vectord)	Get the coefficients for the mu_0, mu_1, mu_2, ..., mu_n terms in the extrapolation algorithm for induced dipoles.
`getForceGroup`((self) -> int)	Get the force group this Force belongs to.
`getInducedDipoles`(self, context)	Get the induced dipole moments of all particles.
`getLabFramePermanentDipoles`(self, context)	Get the fixed dipole moments of all particles in the global reference frame.
`getMultipoleParameters`(self, index)	Get the multipole parameters for a particle.
`getMutualInducedMaxIterations`((self) -> int)	Get the max number of iterations to be used in calculating the mutual induced dipoles
`getMutualInducedTargetEpsilon`((self) -> double)	Get the target epsilon to be used to test for convergence of iterative method used in calculating the mutual induced dipoles
`getNonbondedMethod`(...)	Get the method used for handling long-range nonbonded interactions.
`getNumMultipoles`((self) -> int)	Get the number of particles in the potential function
`getPMEParameters`(self)	Get the parameters to use for PME calculations.
`getPMEParametersInContext`(self, context)	Get the parameters being used for PME in a particular Context.
`getPmeBSplineOrder`((self) -> int)	Get the B-spline order to use for PME charge spreading
`getPmeGridDimensions`(self)	Get the PME grid dimensions.
`getPolarizationType`(...)	Get polarization type
`getSystemMultipoleMoments`(self, context)	Get the system multipole moments.
`getTotalDipoles`(self, context)	Get the total dipole moments (fixed plus induced) of all particles.
`setAEwald`(self, aewald)	Set the Ewald alpha parameter.
`setCovalentMap`(self, index, typeId, ...)	Set the CovalentMap for an atom
`setCutoffDistance`(self, distance)	Set the cutoff distance (in nm) being used for nonbonded interactions.
`setEwaldErrorTolerance`(self, tol)	Get the error tolerance for Ewald summation.
`setExtrapolationCoefficients`(self, coefficients)	Set the coefficients for the mu_0, mu_1, mu_2, ..., mu_n terms in the extrapolation algorithm for induced dipoles.
`setForceGroup`(self, group)	Set the force group this Force belongs to.
`setMultipoleParameters`(self, index, charge, ...)	Set the multipole parameters for a particle.
`setMutualInducedMaxIterations`(self, ...)	Set the max number of iterations to be used in calculating the mutual induced dipoles
`setMutualInducedTargetEpsilon`(self, ...)	Set the target epsilon to be used to test for convergence of iterative method used in calculating the mutual induced dipoles
`setNonbondedMethod`(self, method)	Set the method used for handling long-range nonbonded interactions.
`setPMEParameters`(self, alpha, nx, ny, nz)	Set the parameters to use for PME calculations.
`setPmeGridDimensions`(self, gridDimension)	Set the PME grid dimensions.
`setPolarizationType`(self, type)	Set the polarization type
`updateParametersInContext`(self, context)	Update the multipole parameters in a Context to match those stored in this Force object.
`usesPeriodicBoundaryConditions`((self) -> bool)	Returns whether or not this force makes use of periodic boundary conditions.

Attributes

`Bisector`
`Covalent12`
`Covalent13`
`Covalent14`
`Covalent15`
`CovalentEnd`
`Direct`
`Extrapolated`
`LastAxisTypeIndex`
`Mutual`
`NoAxisType`
`NoCutoff`
`PME`
`PolarizationCovalent11`
`PolarizationCovalent12`
`PolarizationCovalent13`
`PolarizationCovalent14`
`ThreeFold`
`ZBisect`
`ZOnly`
`ZThenX`

getNumMultipoles(self) → int¶: Get the number of particles in the potential function

getNonbondedMethod(self) → OpenMM::AmoebaMultipoleForce::NonbondedMethod¶: Get the method used for handling long-range nonbonded interactions.

setNonbondedMethod(self, method)¶: Set the method used for handling long-range nonbonded interactions.

getPolarizationType(self) → OpenMM::AmoebaMultipoleForce::PolarizationType¶: Get polarization type

setPolarizationType(self, type)¶: Set the polarization type

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.

Returns:	the cutoff distance, measured in nm
Return type:	double

setCutoffDistance(self, 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 (double) – the cutoff distance, measured in nm

getPMEParameters(self)¶

Get the parameters to use for PME calculations. If alpha is 0 (the default), these parameters are ignored and instead their values are chosen based on the Ewald error tolerance.

Returns:	alpha (double) – the separation parameter nx (int) – the number of grid points along the X axis ny (int) – the number of grid points along the Y axis nz (int) – the number of grid points along the Z axis

setPMEParameters(self, alpha, nx, ny, nz)¶

Set the parameters to use for PME calculations. If alpha is 0 (the default), these parameters are ignored and instead their values are chosen based on the Ewald error tolerance.

Parameters:	alpha (double) – the separation parameter nx (int) – the number of grid points along the X axis ny (int) – the number of grid points along the Y axis nz (int) – the number of grid points along the Z axis

getAEwald(self) → double¶

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

Deprecated

This method exists only for backward compatibility. Use getPMEParameters() instead.

Returns:	the Ewald alpha parameter
Return type:	double

setAEwald(self, aewald)¶

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

Deprecated

This method exists only for backward compatibility. Use setPMEParameters() instead.

Parameters:	aewald (double) – alpha parameter

getPmeBSplineOrder(self) → int¶

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

Returns:	the B-spline order
Return type:	int

getPmeGridDimensions(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.

Deprecated

This method exists only for backward compatibility. Use getPMEParameters() instead.

Returns:	the PME grid dimensions
Return type:	void

setPmeGridDimensions(self, 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.

Deprecated

This method exists only for backward compatibility. Use setPMEParameters() instead.

Parameters:	gridDimension (vector< int >) – the PME grid dimensions

getPMEParametersInContext(self, context)¶

Get the parameters being used for PME in a particular Context. Because some platforms have restrictions on the allowed grid sizes, the values that are actually used may be slightly different from those specified with setPmeGridDimensions(), or the standard values calculated based on the Ewald error tolerance. See the manual for details.

Parameters:	context (Context) – the Context for which to get the parameters
Returns:	alpha (double) – the separation parameter nx (int) – the number of grid points along the X axis ny (int) – the number of grid points along the Y axis nz (int) – the number of grid points along the Z axis

addMultipole(self, charge, molecularDipole, molecularQuadrupole, axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY, thole, dampingFactor, polarity) → int¶

Add multipole-related info for a particle

Parameters:	charge (double) – the particle’s charge molecularDipole (vector< double >) – the particle’s molecular dipole (vector of size 3) molecularQuadrupole (vector< double >) – the particle’s molecular quadrupole (vector of size 9) axisType (int) – the particle’s axis type multipoleAtomZ (int) – index of first atom used in constructing lab<->molecular frames multipoleAtomX (int) – index of second atom used in constructing lab<->molecular frames multipoleAtomY (int) – index of second atom used in constructing lab<->molecular frames thole (double) – Thole parameter dampingFactor (double) – dampingFactor parameter polarity (double) – polarity parameter
Returns:	the index of the particle that was added
Return type:	int

getMultipoleParameters(self, index)¶

Get the multipole parameters for a particle.

Parameters: index (int) – the index of the atom for which to get parameters

Returns:

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

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

Set the multipole parameters for a particle.

Parameters:

index (int) – the index of the atom for which to set parameters
charge (double) – the particle’s charge
molecularDipole (vector< double >) – the particle’s molecular dipole (vector of size 3)
molecularQuadrupole (vector< double >) – the particle’s molecular quadrupole (vector of size 9)
axisType (int) – the particle’s axis type
multipoleAtomZ (int) – index of first atom used in constructing lab<->molecular frames
multipoleAtomX (int) – index of second atom used in constructing lab<->molecular frames
multipoleAtomY (int) – index of second atom used in constructing lab<->molecular frames
thole (double) – thole parameter
dampingFactor (double) – damping factor parameter
polarity (double) – polarity parameter

setCovalentMap(self, index, typeId, covalentAtoms)¶

Set the CovalentMap for an atom

Parameters:	index (int) – the index of the atom for which to set parameters typeId (CovalentType) – CovalentTypes type covalentAtoms (vector< int >) – vector of covalent atoms associated w/ the specfied CovalentType

getCovalentMap(self, index, typeId)¶

Get the CovalentMap for an atom

Parameters:	index (int) – the index of the atom for which to set parameters typeId (CovalentType) – CovalentTypes type
Returns:	covalentAtoms – output vector of covalent atoms associated w/ the specfied CovalentType
Return type:	vector< int >

getCovalentMaps(self, index)¶

Get the CovalentMap for an atom

Parameters:	index (int) – the index of the atom for which to set parameters
Returns:	covalentLists – output vector of covalent lists of atoms
Return type:	vector< std::vector< int > >

getMutualInducedMaxIterations(self) → int¶

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

Returns:	max number of iterations
Return type:	int

setMutualInducedMaxIterations(self, inputMutualInducedMaxIterations)¶

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

Parameters:	inputMutualInducedMaxIterations (int) – number of iterations

getMutualInducedTargetEpsilon(self) → double¶

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

Returns:	target epsilon
Return type:	double

setMutualInducedTargetEpsilon(self, inputMutualInducedTargetEpsilon)¶

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

Parameters:	inputMutualInducedTargetEpsilon (double) – target epsilon

setExtrapolationCoefficients(self, coefficients)¶

Set the coefficients for the mu_0, mu_1, mu_2, ..., mu_n terms in the extrapolation algorithm for induced dipoles.

Parameters:	coefficients (vector< double >) – a vector whose mth entry specifies the coefficient for mu_m. The length of this vector determines how many iterations are performed.

getExtrapolationCoefficients(self) → vectord¶: Get the coefficients for the mu_0, mu_1, mu_2, ..., mu_n terms in the extrapolation algorithm for induced dipoles. In this release, the default values for the coefficients are [-0.154, 0.017, 0.658, 0.474], but be aware that those may change in a future release.

getEwaldErrorTolerance(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.

setEwaldErrorTolerance(self, 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.

getLabFramePermanentDipoles(self, context)¶

Get the fixed dipole moments of all particles in the global reference frame.

Parameters:	context (Context) – the Context for which to get the fixed dipoles
Returns:	dipoles – the fixed dipole moment of particle i is stored into the i’th element
Return type:	vector< Vec3 >

getInducedDipoles(self, context)¶

Get the induced dipole moments of all particles.

Parameters:	context (Context) – the Context for which to get the induced dipoles
Returns:	dipoles – the induced dipole moment of particle i is stored into the i’th element
Return type:	vector< Vec3 >

getTotalDipoles(self, context)¶

Get the total dipole moments (fixed plus induced) of all particles.

Parameters:	context (Context) – the Context for which to get the total dipoles
Returns:	dipoles – the total dipole moment of particle i is stored into the i’th element
Return type:	vector< Vec3 >

getElectrostaticPotential(self, inputGrid, context)¶

Get the electrostatic potential.

Parameters:	inputGrid (vector< Vec3 >) – input grid points over which the potential is to be evaluated context (Context) – context
Returns:	outputElectrostaticPotential – output potential
Return type:	vector< double >

getSystemMultipoleMoments(self, context)¶

Get the system multipole moments.

This method is most useful for non-periodic systems. When called for a periodic system, only the <i>lowest nonvanishing moment</i> 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) – context
Returns:	outputMultipoleMoments – (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)
Return type:	vector< double >

updateParametersInContext(self, 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 updateParametersInContext() 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.

usesPeriodicBoundaryConditions(self) → bool¶

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

Returns:	true if nonbondedMethod uses PBC and false otherwise
Return type:	bool

__copy__(self) → Force¶

getForceGroup(self) → int¶: Get the force group this Force belongs to.

setForceGroup(self, group)¶

Set the force group this Force belongs to.

Parameters:	group (int) – the group index. Legal values are between 0 and 31 (inclusive).