- 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 , CustomNonbondedForce
• addForce() : System
• addFunction() : CustomCompoundBondForce , CustomGBForce , CustomHbondForce , CustomNonbondedForce
• addGlobalParameter() : CustomExternalForce , CustomGBForce , CustomHbondForce , CustomNonbondedForce , CustomTorsionForce , CustomAngleForce , CustomBondForce , CustomCompoundBondForce
• addGlobalVariable() : CustomIntegrator
• addInteractionGroup() : CustomNonbondedForce
• addMap() : CMAPTorsionForce
• addMultipole() : AmoebaMultipoleForce
• addOutOfPlaneBend() : AmoebaOutOfPlaneBendForce
• addParticle() : CustomExternalForce , CustomGBForce , CustomNonbondedForce , GBSAOBCForce , GBVIForce , NonbondedForce , System , DrudeForce , AmoebaGeneralizedKirkwoodForce , AmoebaVdwForce , AmoebaWcaDispersionForce
• addPerAcceptorParameter() : CustomHbondForce
• addPerAngleParameter() : CustomAngleForce
• addPerBondParameter() : CustomBondForce , CustomCompoundBondForce
• addPerDofVariable() : CustomIntegrator
• addPerDonorParameter() : CustomHbondForce
• addPerParticleParameter() : CustomExternalForce , CustomGBForce , CustomNonbondedForce
• addPerTorsionParameter() : CustomTorsionForce
• addPiTorsion() : AmoebaPiTorsionForce
• addScreenedPair() : DrudeForce
• addStretchBend() : AmoebaStretchBendForce
• addTorsion() : CMAPTorsionForce , PeriodicTorsionForce , RBTorsionForce , CustomTorsionForce
• 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