GBVIForce Class Reference

This class implements an implicit solvation force using the GB/VI model. More...

Inheritance diagram for GBVIForce:

Public Member Functions
def	getNumParticles
	getNumParticles(GBVIForce self) -> int More...
def	addParticle
	addParticle(GBVIForce self, double charge, double radius, double gamma) -> int More...
def	getParticleParameters
	getParticleParameters(GBVIForce self, int index) More...
def	setParticleParameters
	setParticleParameters(GBVIForce self, int index, double charge, double radius, double gamma) More...
def	addBond
	addBond(GBVIForce self, int particle1, int particle2, double distance) -> int More...
def	getBondParameters
	getBondParameters(GBVIForce self, int index) More...
def	setBondParameters
	setBondParameters(GBVIForce self, int index, int particle1, int particle2, double bondLength) More...
def	getNumBonds
	getNumBonds(GBVIForce self) -> int More...
def	getSolventDielectric
	getSolventDielectric(GBVIForce self) -> double More...
def	setSolventDielectric
	setSolventDielectric(GBVIForce self, double dielectric) More...
def	getSoluteDielectric
	getSoluteDielectric(GBVIForce self) -> double More...
def	setSoluteDielectric
	setSoluteDielectric(GBVIForce self, double dielectric) More...
def	getNonbondedMethod
	getNonbondedMethod(GBVIForce self) -> OpenMM::GBVIForce::NonbondedMethod More...
def	setNonbondedMethod
	setNonbondedMethod(GBVIForce self, OpenMM::GBVIForce::NonbondedMethod method) More...
def	getCutoffDistance
	getCutoffDistance(GBVIForce self) -> double More...
def	setCutoffDistance
	setCutoffDistance(GBVIForce self, double distance) More...
def	getBornRadiusScalingMethod
	getBornRadiusScalingMethod(GBVIForce self) -> OpenMM::GBVIForce::BornRadiusScalingMethod More...
def	setBornRadiusScalingMethod
	setBornRadiusScalingMethod(GBVIForce self, OpenMM::GBVIForce::BornRadiusScalingMethod method) More...
def	getQuinticLowerLimitFactor
	getQuinticLowerLimitFactor(GBVIForce self) -> double More...
def	setQuinticLowerLimitFactor
	setQuinticLowerLimitFactor(GBVIForce self, double quinticLowerLimitFactor) More...
def	getQuinticUpperBornRadiusLimit
	getQuinticUpperBornRadiusLimit(GBVIForce self) -> double More...
def	setQuinticUpperBornRadiusLimit
	setQuinticUpperBornRadiusLimit(GBVIForce self, double quinticUpperBornRadiusLimit) More...
def	usesPeriodicBoundaryConditions
	usesPeriodicBoundaryConditions(GBVIForce self) -> bool More...
def	__init__
	init(OpenMM::GBVIForce self) -> GBVIForce init(OpenMM::GBVIForce self, GBVIForce other) -> GBVIForce More...
def	__del__
	del(OpenMM::GBVIForce 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

Static Public Attributes
	NoCutoff = _openmm.GBVIForce_NoCutoff
	CutoffNonPeriodic = _openmm.GBVIForce_CutoffNonPeriodic
	CutoffPeriodic = _openmm.GBVIForce_CutoffPeriodic
	NoScaling = _openmm.GBVIForce_NoScaling
	QuinticSpline = _openmm.GBVIForce_QuinticSpline

Detailed Description

This class implements an implicit solvation force using the GB/VI model.

To use this class, create a GBVIForce object, then call addParticle() once for each particle in the System to define its parameters. The number of particles for which you define GB/VI parameters must be exactly 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().

Constructor & Destructor Documentation

def __init__	(		self,
			args
	)

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

This class implements an implicit solvation force using the GB/VI model.

To use this class, create a GBVIForce object, then call addParticle() once for each particle in the System to define its parameters. The number of particles for which you define GB/VI parameters must be exactly 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().

References simtk.openmm.openmm.stripUnits().

def __del__

(

self

)

del(OpenMM::GBVIForce self)

References simtk.openmm.openmm.stripUnits().

Member Function Documentation

def addBond	(		self,
			args
	)

addBond(GBVIForce self, int particle1, int particle2, double distance) -> int

Add a bond

Parameters

particle1	the index of the first particle
particle2	the index of the second particle
distance	the distance between the two particles, measured in nm

References simtk.openmm.openmm.stripUnits().

Referenced by Topology.createDisulfideBonds(), and Topology.createStandardBonds().

def addParticle	(		self,
			args
	)

addParticle(GBVIForce self, double charge, double radius, double gamma) -> int

Add the GB/VI 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	the charge of the particle, measured in units of the proton charge
radius	the GB/VI radius of the particle, measured in nm
gamma	the gamma parameter

References simtk.openmm.openmm.stripUnits().

Referenced by NonbondedForce.addParticle_usingRVdw().

def getBondParameters	(		self,
			args
	)

getBondParameters(GBVIForce self, int index)

Get the parameters defining a bond

Parameters

index	the index of the bond for which to get parameters
particle1	the index of the first particle involved in the bond
particle2	the index of the second particle involved in the bond
distance	the distance between the two particles, measured in nm

References simtk.openmm.openmm.stripUnits().

def getBornRadiusScalingMethod	(		self,
			args
	)

getBornRadiusScalingMethod(GBVIForce self) -> OpenMM::GBVIForce::BornRadiusScalingMethod

Get Born radius scaling method

References simtk.openmm.openmm.stripUnits().

def getCutoffDistance	(		self,
			args
	)

getCutoffDistance(GBVIForce 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 getNonbondedMethod	(		self,
			args
	)

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

Get the method used for handling long range nonbonded interactions.

References simtk.openmm.openmm.stripUnits().

def getNumBonds	(		self,
			args
	)

getNumBonds(GBVIForce self) -> int

Get number of bonds

References simtk.openmm.openmm.stripUnits().

def getNumParticles	(		self,
			args
	)

getNumParticles(GBVIForce self) -> int

Get the number of particles in the system.

References simtk.openmm.openmm.stripUnits().

def getParticleParameters	(		self,
			args
	)

getParticleParameters(GBVIForce self, int index)

Get the force field parameters for a particle.

Parameters

index	the index of the particle for which to get parameters
charge	the charge of the particle, measured in units of the proton charge
radius	the GBSA radius of the particle, measured in nm
gamma	the gamma parameter

References simtk.openmm.openmm.stripUnits().

def getQuinticLowerLimitFactor	(		self,
			args
	)

getQuinticLowerLimitFactor(GBVIForce self) -> double

Get the lower limit factor used in the quintic spline scaling method (typically 0.5-0.8)

References simtk.openmm.openmm.stripUnits().

def getQuinticUpperBornRadiusLimit	(		self,
			args
	)

getQuinticUpperBornRadiusLimit(GBVIForce self) -> double

Get the upper limit used in the quintic spline scaling method, measured in nm (~5.0)

References simtk.openmm.openmm.stripUnits().

def getSoluteDielectric	(		self,
			args
	)

getSoluteDielectric(GBVIForce self) -> double

Get the dielectric constant for the solute.

References simtk.openmm.openmm.stripUnits().

def getSolventDielectric	(		self,
			args
	)

getSolventDielectric(GBVIForce self) -> double

Get the dielectric constant for the solvent.

References simtk.openmm.openmm.stripUnits().

def setBondParameters	(		self,
			args
	)

setBondParameters(GBVIForce self, int index, int particle1, int particle2, double bondLength)

Set 1-2 bonds

Parameters

index	index of the bond for which to set parameters
particle1	index of first atom in bond
particle2	index of second atom in bond
bondLength	bond length, measured in nm

References simtk.openmm.openmm.stripUnits().

def setBornRadiusScalingMethod	(		self,
			args
	)

setBornRadiusScalingMethod(GBVIForce self, OpenMM::GBVIForce::BornRadiusScalingMethod method)

Set Born radius scaling method

References simtk.openmm.openmm.stripUnits().

def setCutoffDistance	(		self,
			args
	)

setCutoffDistance(GBVIForce 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 setNonbondedMethod	(		self,
			args
	)

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

Set the method used for handling long range nonbonded interactions.

References simtk.openmm.openmm.stripUnits().

def setParticleParameters	(		self,
			args
	)

setParticleParameters(GBVIForce self, int index, double charge, double radius, double gamma)

Set the force field parameters for a particle.

Parameters

index	the index of the particle for which to set parameters
charge	the charge of the particle, measured in units of the proton charge
radius	the GB/VI radius of the particle, measured in nm
gamma	the gamma parameter

References simtk.openmm.openmm.stripUnits().

def setQuinticLowerLimitFactor	(		self,
			args
	)

setQuinticLowerLimitFactor(GBVIForce self, double quinticLowerLimitFactor)

Set the lower limit factor used in the quintic spline scaling method (typically 0.5-0.8)

References simtk.openmm.openmm.stripUnits().

def setQuinticUpperBornRadiusLimit	(		self,
			args
	)

setQuinticUpperBornRadiusLimit(GBVIForce self, double quinticUpperBornRadiusLimit)

Set the upper limit used in the quintic spline scaling method, measured in nm (~5.0)

References simtk.openmm.openmm.stripUnits().

def setSoluteDielectric	(		self,
			args
	)

setSoluteDielectric(GBVIForce self, double dielectric)

Set the dielectric constant for the solute.

References simtk.openmm.openmm.stripUnits().

def setSolventDielectric	(		self,
			args
	)

setSolventDielectric(GBVIForce self, double dielectric)

Set the dielectric constant for the solvent.

References simtk.openmm.openmm.stripUnits().

def usesPeriodicBoundaryConditions	(		self,
			args
	)

usesPeriodicBoundaryConditions(GBVIForce self) -> bool

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

References simtk.openmm.openmm.stripUnits().

Member Data Documentation

CutoffNonPeriodic = _openmm.GBVIForce_CutoffNonPeriodic

static

CutoffPeriodic = _openmm.GBVIForce_CutoffPeriodic

static

NoCutoff = _openmm.GBVIForce_NoCutoff

static

NoScaling = _openmm.GBVIForce_NoScaling

static

QuinticSpline = _openmm.GBVIForce_QuinticSpline

static

this

Referenced by System.__init__().

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

• openmm.py