AmoebaGeneralizedKirkwoodForce Class Reference

This class implements an implicit solvation force using the generalized Kirkwood/Grycuk model. More...

Inheritance diagram for AmoebaGeneralizedKirkwoodForce:

List of all members.

Public Member Functions
def	getNumParticles
	getNumParticles(self) -> int
def	addParticle
	addParticle(self, charge, radius, scalingFactor) -> int
def	getParticleParameters
	Get the force field parameters for a particle.
def	setParticleParameters
	Set the force field parameters for a particle.
def	getSolventDielectric
	getSolventDielectric(self) -> double
def	setSolventDielectric
	Set the dielectric constant for the solvent.
def	getSoluteDielectric
	getSoluteDielectric(self) -> double
def	setSoluteDielectric
	Set the dielectric constant for the solute.
def	getIncludeCavityTerm
	getIncludeCavityTerm(self) -> int
def	setIncludeCavityTerm
	Set the flag signaling whether the cavity term should be included.
def	getProbeRadius
	getProbeRadius(self) -> double
def	setProbeRadius
	Set the probe radius (nm) used in SASA contribution.
def	getSurfaceAreaFactor
	getSurfaceAreaFactor(self) -> double
def	setSurfaceAreaFactor
	Set the surface area factor kJ/(nm*nm) used in SASA contribution.
def	updateParametersInContext
	Update the per-particle parameters in a Context to match those stored in this Force object.
def	usesPeriodicBoundaryConditions
	usesPeriodicBoundaryConditions(self) -> bool
def	__init__
	__init__(self) -> AmoebaGeneralizedKirkwoodForce __init__(self, other) -> AmoebaGeneralizedKirkwoodForce
Public Attributes
	this

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Detailed Description

This class implements an implicit solvation force using the generalized Kirkwood/Grycuk model.

To use this class, create an AmoebaGeneralizedKirkwoodForce object, then call addParticle() once for each particle in the System to define its parameters. The number of particles for which you define parameters must be equal to the number of particles in the System, or else an exception will be thrown when you try to create a Context. After a particle has been added, you can modify its force field parameters by calling setParticleParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

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Constructor & Destructor Documentation

def __init__	(		self,
			args
	)

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

This class implements an implicit solvation force using the generalized Kirkwood/Grycuk model.

To use this class, create an AmoebaGeneralizedKirkwoodForce object, then call addParticle() once for each particle in the System to define its parameters. The number of particles for which you define parameters must be equal to the number of particles in the System, or else an exception will be thrown when you try to create a Context. After a particle has been added, you can modify its force field parameters by calling setParticleParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

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Member Function Documentation

def addParticle	(		self,
			charge,
			radius,
			scalingFactor
	)

addParticle(self, charge, radius, scalingFactor) -> int

Add the parameters for a particle. This should be called once for each particle in the System. When it is called for the i'th time, it specifies the parameters for the i'th particle.

Parameters:

charge	(double) the charge of the particle, measured in units of the proton charge
radius	(double) the atomic radius of the particle, measured in nm
scalingFactor	(double) the scaling factor for the particle

Returns:

(int) the index of the particle that was added

def getIncludeCavityTerm

(

self

)

getIncludeCavityTerm(self) -> int

Get the flag signaling whether the cavity term should be included

def getNumParticles

(

self

)

getNumParticles(self) -> int

Get the number of particles in the system.

def getParticleParameters	(		self,
			index
	)

Get the force field parameters for a particle.

Parameters:

index

(int) the index of the particle for which to get parameters

Returns:

(double) the charge of the particle, measured in units of the proton charge

(double) the atomic radius of the particle, measured in nm

(double) the scaling factor for the particle

def getProbeRadius

(

self

)

getProbeRadius(self) -> double

Get the probe radius (nm) used in SASA contribution

def getSoluteDielectric

(

self

)

getSoluteDielectric(self) -> double

Get the dielectric constant for the solute.

def getSolventDielectric

(

self

)

getSolventDielectric(self) -> double

Get the dielectric constant for the solvent.

def getSurfaceAreaFactor

(

self

)

getSurfaceAreaFactor(self) -> double

Get the surface area factor kJ/(nm*nm) used in SASA contribution

def setIncludeCavityTerm	(		self,
			includeCavityTerm
	)

Set the flag signaling whether the cavity term should be included.

def setParticleParameters	(		self,
			index,
			charge,
			radius,
			scalingFactor
	)

Set the force field parameters for a particle.

Parameters:

index	(int) the index of the particle for which to set parameters
charge	(double) the charge of the particle, measured in units of the proton charge
radius	(double) the atomic radius of the particle, measured in nm
scalingFactor	(double) the scaling factor for the particle

def setProbeRadius	(		self,
			probeRadius
	)

Set the probe radius (nm) used in SASA contribution.

def setSoluteDielectric	(		self,
			dielectric
	)

Set the dielectric constant for the solute.

def setSolventDielectric	(		self,
			dielectric
	)

Set the dielectric constant for the solvent.

def setSurfaceAreaFactor	(		self,
			surfaceAreaFactor
	)

Set the surface area factor kJ/(nm*nm) used in SASA contribution.

def updateParametersInContext	(		self,
			context
	)

Update the per-particle 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 setParticleParameters() to modify this object's parameters, then call updateParametersInContext() to copy them over to the Context.

The only information this method updates is the values of per-particle parameters. All other aspects of the Force (the probe radius, the surface area factor, etc.) are unaffected and can only be changed by reinitializing the Context.

def usesPeriodicBoundaryConditions

(

self

)

usesPeriodicBoundaryConditions(self) -> bool

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

Returns:

(bool) true if nonbondedMethod uses PBC and false otherwise

Reimplemented from Force.

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Member Data Documentation

this

Reimplemented from Force.

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

• openmm.py