GBSAOBCForce Class Reference

This class implements an implicit solvation force using the GBSA-OBC model. More...

Inheritance diagram for GBSAOBCForce:

Public Member Functions
def	getNumParticles
	getNumParticles(GBSAOBCForce self) -> int More...
def	addParticle
	addParticle(GBSAOBCForce self, double charge, double radius, double scalingFactor) -> int More...
def	getParticleParameters
	getParticleParameters(GBSAOBCForce self, int index) More...
def	setParticleParameters
	setParticleParameters(GBSAOBCForce self, int index, double charge, double radius, double scalingFactor) More...
def	getSolventDielectric
	getSolventDielectric(GBSAOBCForce self) -> double More...
def	setSolventDielectric
	setSolventDielectric(GBSAOBCForce self, double dielectric) More...
def	getSoluteDielectric
	getSoluteDielectric(GBSAOBCForce self) -> double More...
def	setSoluteDielectric
	setSoluteDielectric(GBSAOBCForce self, double dielectric) More...
def	getSurfaceAreaEnergy
	getSurfaceAreaEnergy(GBSAOBCForce self) -> double More...
def	setSurfaceAreaEnergy
	setSurfaceAreaEnergy(GBSAOBCForce self, double energy) More...
def	getNonbondedMethod
	getNonbondedMethod(GBSAOBCForce self) -> OpenMM::GBSAOBCForce::NonbondedMethod More...
def	setNonbondedMethod
	setNonbondedMethod(GBSAOBCForce self, OpenMM::GBSAOBCForce::NonbondedMethod method) More...
def	getCutoffDistance
	getCutoffDistance(GBSAOBCForce self) -> double More...
def	setCutoffDistance
	setCutoffDistance(GBSAOBCForce self, double distance) More...
def	updateParametersInContext
	updateParametersInContext(GBSAOBCForce self, Context context) More...
def	usesPeriodicBoundaryConditions
	usesPeriodicBoundaryConditions(GBSAOBCForce self) -> bool More...
def	__init__
	init(OpenMM::GBSAOBCForce self) -> GBSAOBCForce init(OpenMM::GBSAOBCForce self, GBSAOBCForce other) -> GBSAOBCForce More...
def	__del__
	del(OpenMM::GBSAOBCForce 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.GBSAOBCForce_NoCutoff
	CutoffNonPeriodic = _openmm.GBSAOBCForce_CutoffNonPeriodic
	CutoffPeriodic = _openmm.GBSAOBCForce_CutoffPeriodic

Detailed Description

This class implements an implicit solvation force using the GBSA-OBC model.

To use this class, create a GBSAOBCForce object, then call addParticle() once for each particle in the System to define its parameters. The number of particles for which you define GBSA 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(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

When using this Force, the System should also include a NonbondedForce, and both objects must specify identical charges for all particles. Otherwise, the results will not be correct. Furthermore, if the nonbonded method is set to CutoffNonPeriodic or CutoffPeriodic, you should call setReactionFieldDielectric(1.0) on the NonbondedForce to turn off the reaction field approximation, which does not produce correct results when combined with GBSA.

Constructor & Destructor Documentation

def __init__	(		self,
			args
	)

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

Create a GBSAOBCForce.

References simtk.openmm.openmm.stripUnits().

def __del__

(

self

)

del(OpenMM::GBSAOBCForce self)

References simtk.openmm.openmm.stripUnits().

Member Function Documentation

def addParticle	(		self,
			args
	)

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

Add the GBSA 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 GBSA radius of the particle, measured in nm
scalingFactor	the OBC scaling factor for the particle

References simtk.openmm.openmm.stripUnits().

Referenced by NonbondedForce.addParticle_usingRVdw().

def getCutoffDistance	(		self,
			args
	)

getCutoffDistance(GBSAOBCForce 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(GBSAOBCForce self) -> OpenMM::GBSAOBCForce::NonbondedMethod

Get the method used for handling long range nonbonded interactions.

References simtk.openmm.openmm.stripUnits().

def getNumParticles	(		self,
			args
	)

getNumParticles(GBSAOBCForce self) -> int

Get the number of particles in the system.

References simtk.openmm.openmm.stripUnits().

def getParticleParameters	(		self,
			args
	)

getParticleParameters(GBSAOBCForce 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
scalingFactor	the OBC scaling factor for the particle

References simtk.openmm.openmm.stripUnits().

def getSoluteDielectric	(		self,
			args
	)

getSoluteDielectric(GBSAOBCForce self) -> double

Get the dielectric constant for the solute.

References simtk.openmm.openmm.stripUnits().

def getSolventDielectric	(		self,
			args
	)

getSolventDielectric(GBSAOBCForce self) -> double

Get the dielectric constant for the solvent.

References simtk.openmm.openmm.stripUnits().

def getSurfaceAreaEnergy	(		self,
			args
	)

getSurfaceAreaEnergy(GBSAOBCForce self) -> double

Get the energy scale for the surface energy term, measured in kJ/mol/nm^2.

References simtk.openmm.openmm.stripUnits().

def setCutoffDistance	(		self,
			args
	)

setCutoffDistance(GBSAOBCForce 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(GBSAOBCForce self, OpenMM::GBSAOBCForce::NonbondedMethod method)

Set the method used for handling long range nonbonded interactions.

References simtk.openmm.openmm.stripUnits().

def setParticleParameters	(		self,
			args
	)

setParticleParameters(GBSAOBCForce self, int index, double charge, double radius, double scalingFactor)

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 GBSA radius of the particle, measured in nm
scalingFactor	the OBC scaling factor for the particle

References simtk.openmm.openmm.stripUnits().

def setSoluteDielectric	(		self,
			args
	)

setSoluteDielectric(GBSAOBCForce self, double dielectric)

Set the dielectric constant for the solute.

References simtk.openmm.openmm.stripUnits().

def setSolventDielectric	(		self,
			args
	)

setSolventDielectric(GBSAOBCForce self, double dielectric)

Set the dielectric constant for the solvent.

References simtk.openmm.openmm.stripUnits().

def setSurfaceAreaEnergy	(		self,
			args
	)

setSurfaceAreaEnergy(GBSAOBCForce self, double energy)

Set the energy scale for the surface energy term, measured in kJ/mol/nm^2.

References simtk.openmm.openmm.stripUnits().

def updateParametersInContext	(		self,
			args
	)

updateParametersInContext(GBSAOBCForce self, Context context)

Update the 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 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 particles, only to change the parameters of existing ones.

References simtk.openmm.openmm.stripUnits().

def usesPeriodicBoundaryConditions	(		self,
			args
	)

usesPeriodicBoundaryConditions(GBSAOBCForce self) -> bool

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

References simtk.openmm.openmm.stripUnits().

Member Data Documentation

CutoffNonPeriodic = _openmm.GBSAOBCForce_CutoffNonPeriodic

static

CutoffPeriodic = _openmm.GBSAOBCForce_CutoffPeriodic

static

NoCutoff = _openmm.GBSAOBCForce_NoCutoff

static

this

Referenced by System.__init__().

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

• openmm.py