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OpenMM
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OpenMM
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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 | |
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().
| def __init__ | ( | self, | |
| args | |||
| ) |
| def __del__ | ( | self | ) |
del(OpenMM::GBVIForce self)
| def addBond | ( | self, | |
| args | |||
| ) |
addBond(GBVIForce self, int particle1, int particle2, double distance) -> int
Add a bond
| 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(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.
| 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 |
| def getBondParameters | ( | self, | |
| args | |||
| ) |
getBondParameters(GBVIForce self, int index)
Get the parameters defining a bond
| 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(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.
| 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 |
| 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
| 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 |
| 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.
| distance | the 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.
| 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 |
| 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.
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