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

def __del__ (   self)

del(OpenMM::GBVIForce self)

Member Function Documentation

def addBond (   self,
  args 
)

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

Add a bond

Parameters
particle1the index of the first particle
particle2the index of the second particle
distancethe distance between the two particles, measured in nm
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
chargethe charge of the particle, measured in units of the proton charge
radiusthe GB/VI radius of the particle, measured in nm
gammathe gamma parameter
def getBondParameters (   self,
  args 
)

getBondParameters(GBVIForce self, int index)

Get the parameters defining a bond

Parameters
indexthe index of the bond for which to get parameters
particle1the index of the first particle involved in the bond
particle2the index of the second particle involved in the bond
distancethe distance between the two particles, measured in nm
def getBornRadiusScalingMethod (   self)

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

Get Born radius scaling method

def getCutoffDistance (   self)

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.

def getNonbondedMethod (   self)

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

Get the method used for handling long range nonbonded interactions.

def getNumBonds (   self)

getNumBonds(GBVIForce self) -> int

Get number of bonds

def getNumParticles (   self)

getNumParticles(GBVIForce self) -> int

Get the number of particles in the system.

def getParticleParameters (   self,
  args 
)

getParticleParameters(GBVIForce self, int index)

Get the force field parameters for a particle.

Parameters
indexthe index of the particle for which to get parameters
chargethe charge of the particle, measured in units of the proton charge
radiusthe GBSA radius of the particle, measured in nm
gammathe gamma parameter
def getQuinticLowerLimitFactor (   self)

getQuinticLowerLimitFactor(GBVIForce self) -> double

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

def getQuinticUpperBornRadiusLimit (   self)

getQuinticUpperBornRadiusLimit(GBVIForce self) -> double

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

def getSoluteDielectric (   self)

getSoluteDielectric(GBVIForce self) -> double

Get the dielectric constant for the solute.

def getSolventDielectric (   self)

getSolventDielectric(GBVIForce self) -> double

Get the dielectric constant for the solvent.

def setBondParameters (   self,
  args 
)

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

Set 1-2 bonds

Parameters
indexindex of the bond for which to set parameters
particle1index of first atom in bond
particle2index of second atom in bond
bondLengthbond length, measured in nm
def setBornRadiusScalingMethod (   self,
  args 
)

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

Set Born radius scaling method

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
distancethe cutoff distance, measured in nm
def setNonbondedMethod (   self,
  args 
)

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

Set the method used for handling long range nonbonded interactions.

def setParticleParameters (   self,
  args 
)

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

Set the force field parameters for a particle.

Parameters
indexthe index of the particle for which to set parameters
chargethe charge of the particle, measured in units of the proton charge
radiusthe GB/VI radius of the particle, measured in nm
gammathe gamma parameter
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)

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)

def setSoluteDielectric (   self,
  args 
)

setSoluteDielectric(GBVIForce self, double dielectric)

Set the dielectric constant for the solute.

def setSolventDielectric (   self,
  args 
)

setSolventDielectric(GBVIForce self, double dielectric)

Set the dielectric constant for the solvent.

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

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