### - a -

- addAcceptor() : CustomHbondForce
- addAngle() : CustomAngleForce , AmoebaAngleForce , AmoebaInPlaneAngleForce , HarmonicAngleForce
- addBond() : GBVIForce , HarmonicBondForce , AmoebaBondForce , CustomBondForce , CustomCompoundBondForce
- addComputedValue() : CustomGBForce
- addComputeGlobal() : CustomIntegrator
- addComputePerDof() : CustomIntegrator
- addComputeSum() : CustomIntegrator
- addConstrainPositions() : CustomIntegrator
- addConstraint() : System
- addConstrainVelocities() : CustomIntegrator
- addDonor() : CustomHbondForce
- addEnergyTerm() : CustomGBForce
- addException() : NonbondedForce
- addExclusion() : CustomGBForce , CustomHbondForce , CustomManyParticleForce , CustomNonbondedForce
- addForce() : System
- addFunction() : CustomCompoundBondForce , CustomGBForce , CustomHbondForce , CustomNonbondedForce
- addGlobalParameter() : CustomCompoundBondForce , CustomExternalForce , CustomGBForce , CustomHbondForce , CustomManyParticleForce , CustomNonbondedForce , CustomTorsionForce , CustomAngleForce , CustomBondForce
- addGlobalVariable() : CustomIntegrator
- addInteractionGroup() : CustomNonbondedForce
- addMap() : CMAPTorsionForce
- addMultipole() : AmoebaMultipoleForce
- addOutOfPlaneBend() : AmoebaOutOfPlaneBendForce
- addParticle() : CustomExternalForce , CustomGBForce , CustomManyParticleForce , CustomNonbondedForce , GBSAOBCForce , GBVIForce , NonbondedForce , System , DrudeForce , AmoebaGeneralizedKirkwoodForce , AmoebaVdwForce , AmoebaWcaDispersionForce
- addPerAcceptorParameter() : CustomHbondForce
- addPerAngleParameter() : CustomAngleForce
- addPerBondParameter() : CustomCompoundBondForce , CustomBondForce
- addPerDofVariable() : CustomIntegrator
- addPerDonorParameter() : CustomHbondForce
- addPerParticleParameter() : CustomGBForce , CustomManyParticleForce , CustomNonbondedForce , CustomExternalForce
- addPerTorsionParameter() : CustomTorsionForce
- addPiTorsion() : AmoebaPiTorsionForce
- addScreenedPair() : DrudeForce
- addStretchBend() : AmoebaStretchBendForce
- addTabulatedFunction() : CustomCompoundBondForce , CustomHbondForce , CustomManyParticleForce , CustomNonbondedForce , CustomGBForce
- addTorsion() : PeriodicTorsionForce , CMAPTorsionForce , CustomTorsionForce , RBTorsionForce
- addTorsionTorsion() : AmoebaTorsionTorsionForce
- addUpdateContextState() : CustomIntegrator
- AmoebaAngleForce() : AmoebaAngleForce
- AmoebaAngleForceImpl() : AmoebaAngleForceImpl
- AmoebaBondForce() : AmoebaBondForce
- AmoebaBondForceImpl() : AmoebaBondForceImpl
- AmoebaGeneralizedKirkwoodForce() : AmoebaGeneralizedKirkwoodForce
- AmoebaGeneralizedKirkwoodForceImpl() : AmoebaGeneralizedKirkwoodForceImpl
- AmoebaInPlaneAngleForce() : AmoebaInPlaneAngleForce
- AmoebaInPlaneAngleForceImpl() : AmoebaInPlaneAngleForceImpl
- AmoebaMultipoleForce() : AmoebaMultipoleForce
- AmoebaMultipoleForceImpl() : AmoebaMultipoleForceImpl
- AmoebaOutOfPlaneBendForce() : AmoebaOutOfPlaneBendForce
- AmoebaOutOfPlaneBendForceImpl() : AmoebaOutOfPlaneBendForceImpl
- AmoebaPiTorsionForce() : AmoebaPiTorsionForce
- AmoebaPiTorsionForceImpl() : AmoebaPiTorsionForceImpl
- AmoebaStretchBendForce() : AmoebaStretchBendForce
- AmoebaStretchBendForceImpl() : AmoebaStretchBendForceImpl
- AmoebaTorsionTorsionForce() : AmoebaTorsionTorsionForce
- AmoebaTorsionTorsionForceImpl() : AmoebaTorsionTorsionForceImpl
- AmoebaVdwForce() : AmoebaVdwForce
- AmoebaVdwForceImpl() : AmoebaVdwForceImpl
- AmoebaWcaDispersionForce() : AmoebaWcaDispersionForce
- AmoebaWcaDispersionForceImpl() : AmoebaWcaDispersionForceImpl
- AndersenThermostat() : AndersenThermostat
- AndersenThermostatImpl() : AndersenThermostatImpl
- applyConstraints() : Context , ContextImpl
- applyVelocityConstraints() : ContextImpl , Context