GBVISoftcoreForce Class Reference
This class implements an implicit solvation force using the GB/VI model. More...
Public Member Functions | |
| def | getNumParticles |
| getNumParticles(self) -> int | |
| def | addParticle |
| addParticle(self, double charge, double radius, double gamma, double bornRadiusScaleFactor = 1.0) addParticle(self, double charge, double radius, double gamma) | |
| def | getParticleParameters |
| getParticleParameters(self, int index) | |
| def | setParticleParameters |
| setParticleParameters(self, int index, double charge, double radius, double gamma, double bornRadiusScaleFactor = 1.0) setParticleParameters(self, int index, double charge, double radius, double gamma) | |
| def | addBond |
| addBond(self, int particle1, int particle2, double distance) -> int | |
| def | getBondParameters |
| getBondParameters(self, int index) | |
| def | setBondParameters |
| setBondParameters(self, int index, int particle1, int particle2, double bondLength) | |
| def | getNumBonds |
| getNumBonds(self) -> int | |
| def | getSolventDielectric |
| getSolventDielectric(self) -> double | |
| def | setSolventDielectric |
| setSolventDielectric(self, double dielectric) | |
| def | getSoluteDielectric |
| getSoluteDielectric(self) -> double | |
| def | setSoluteDielectric |
| setSoluteDielectric(self, double dielectric) | |
| def | getNonbondedMethod |
| getNonbondedMethod(self) -> NonbondedSoftcoreMethod | |
| def | setNonbondedMethod |
| setNonbondedMethod(self, NonbondedSoftcoreMethod method) | |
| def | getCutoffDistance |
| getCutoffDistance(self) -> double | |
| def | setCutoffDistance |
| setCutoffDistance(self, double distance) | |
| def | getBornRadiusScalingMethod |
| getBornRadiusScalingMethod(self) -> BornRadiusScalingSoftcoreMethod | |
| def | setBornRadiusScalingMethod |
| setBornRadiusScalingMethod(self, BornRadiusScalingSoftcoreMethod method) | |
| def | getQuinticLowerLimitFactor |
| getQuinticLowerLimitFactor(self) -> double | |
| def | setQuinticLowerLimitFactor |
| setQuinticLowerLimitFactor(self, double quinticLowerLimitFactor) | |
| def | getQuinticUpperBornRadiusLimit |
| getQuinticUpperBornRadiusLimit(self) -> double | |
| def | setQuinticUpperBornRadiusLimit |
| setQuinticUpperBornRadiusLimit(self, double quinticUpperBornRadiusLimit) | |
| def | __init__ |
| __init__(self) -> GBVISoftcoreForce __init__(self, GBVISoftcoreForce other) -> GBVISoftcoreForce | |
| def | __del__ |
| __del__(self) | |
Public Attributes | |
| this | |
Static Public Attributes | |
| NoCutoff = _openmm.GBVISoftcoreForce_NoCutoff | |
| CutoffNonPeriodic = _openmm.GBVISoftcoreForce_CutoffNonPeriodic | |
| CutoffPeriodic = _openmm.GBVISoftcoreForce_CutoffPeriodic | |
| NoScaling = _openmm.GBVISoftcoreForce_NoScaling | |
| QuinticSpline = _openmm.GBVISoftcoreForce_QuinticSpline | |
Detailed Description
This class implements an implicit solvation force using the GB/VI model.
To use this class, create a GBVISoftcoreForce 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 an Context. After a particle has been added, you can modify its force field parameters by calling setParticleParameters().
If the System also contains a NonbondedForce, this force will use the cutoffs and periodic boundary conditions specified in it.
Member Function Documentation
| def __del__ | ( | self | ) |
__del__(self)
Reimplemented from Force.
| def __init__ | ( | self, | ||
| args | ||||
| ) |
__init__(self) -> GBVISoftcoreForce __init__(self, GBVISoftcoreForce other) -> GBVISoftcoreForce
| def addBond | ( | self, | ||
| args | ||||
| ) |
addBond(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
| def addParticle | ( | self, | ||
| args | ||||
| ) |
addParticle(self, double charge, double radius, double gamma, double bornRadiusScaleFactor = 1.0) addParticle(self, double charge, double radius, double gamma)
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 bornRadiusScaleFactor the Born radius scale factor (used for free energy calculations)
| def getBondParameters | ( | self, | ||
| args | ||||
| ) |
getBondParameters(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
| def getBornRadiusScalingMethod | ( | self | ) |
getBornRadiusScalingMethod(self) -> BornRadiusScalingSoftcoreMethod
Get the method used for scaling Born radii.
| def getCutoffDistance | ( | self | ) |
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.
| def getNonbondedMethod | ( | self | ) |
getNonbondedMethod(self) -> NonbondedSoftcoreMethod
Get the method used for handling long range nonbonded interactions.
| def getNumBonds | ( | self | ) |
getNumBonds(self) -> int
Get number of bonds
| def getNumParticles | ( | self | ) |
getNumParticles(self) -> int
Get the number of particles in the system.
| def getParticleParameters | ( | self, | ||
| args | ||||
| ) |
getParticleParameters(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 bornRadiusScaleFactor the Born radius scale factor (used for free energy calculations)
| def getQuinticLowerLimitFactor | ( | self | ) |
getQuinticLowerLimitFactor(self) -> double
Get the lower limit factor used in the quintic spline scaling method (typically 0.5-0.8)
| def getQuinticUpperBornRadiusLimit | ( | self | ) |
getQuinticUpperBornRadiusLimit(self) -> double
Get the upper limit used in the quintic spline scaling method (typically 0.5-0.8)
| 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 setBondParameters | ( | self, | ||
| args | ||||
| ) |
setBondParameters(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
| def setBornRadiusScalingMethod | ( | self, | ||
| args | ||||
| ) |
setBornRadiusScalingMethod(self, BornRadiusScalingSoftcoreMethod method)
Set the method used for scaling Born radii.
| def setCutoffDistance | ( | self, | ||
| args | ||||
| ) |
setCutoffDistance(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.
| def setNonbondedMethod | ( | self, | ||
| args | ||||
| ) |
setNonbondedMethod(self, NonbondedSoftcoreMethod method)
Set the method used for handling long range nonbonded interactions.
| def setParticleParameters | ( | self, | ||
| args | ||||
| ) |
setParticleParameters(self, int index, double charge, double radius, double gamma, double bornRadiusScaleFactor = 1.0) setParticleParameters(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 bornRadiusScaleFactor the Born radius scale factor (used for free energy calculations)
| def setQuinticLowerLimitFactor | ( | self, | ||
| args | ||||
| ) |
setQuinticLowerLimitFactor(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(self, double quinticUpperBornRadiusLimit)
Set the upper limit used in the quintic spline scaling method (typically 0.008)
| def setSoluteDielectric | ( | self, | ||
| args | ||||
| ) |
setSoluteDielectric(self, double dielectric)
Set the dielectric constant for the solute.
| def setSolventDielectric | ( | self, | ||
| args | ||||
| ) |
setSolventDielectric(self, double dielectric)
Set the dielectric constant for the solvent.
Member Data Documentation
CutoffNonPeriodic = _openmm.GBVISoftcoreForce_CutoffNonPeriodic [static] |
CutoffPeriodic = _openmm.GBVISoftcoreForce_CutoffPeriodic [static] |
NoCutoff = _openmm.GBVISoftcoreForce_NoCutoff [static] |
NoScaling = _openmm.GBVISoftcoreForce_NoScaling [static] |
QuinticSpline = _openmm.GBVISoftcoreForce_QuinticSpline [static] |
The documentation for this class was generated from the following file:
- openmm.py
