- a -

• addAcceptor() : CustomHbondForce
• addAngle() : CustomAngleForce , HarmonicAngleForce
• addBond() : CustomBondForce , CustomCompoundBondForce , GBVIForce , HarmonicBondForce
• 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() : CustomNonbondedForce , CustomTorsionForce , CustomAngleForce , CustomBondForce , CustomCompoundBondForce , CustomExternalForce , CustomGBForce , CustomHbondForce
• addGlobalVariable() : CustomIntegrator
• addMap() : CMAPTorsionForce
• addParticle() : GBSAOBCForce , CustomExternalForce , CustomGBForce , CustomNonbondedForce , GBVIForce , NonbondedForce , System
• addPerAcceptorParameter() : CustomHbondForce
• addPerAngleParameter() : CustomAngleForce
• addPerBondParameter() : CustomBondForce , CustomCompoundBondForce
• addPerDofVariable() : CustomIntegrator
• addPerDonorParameter() : CustomHbondForce
• addPerParticleParameter() : CustomGBForce , CustomExternalForce , CustomNonbondedForce
• addPerTorsionParameter() : CustomTorsionForce
• addTorsion() : CMAPTorsionForce , RBTorsionForce , CustomTorsionForce , PeriodicTorsionForce
• addUpdateContextState() : CustomIntegrator
• AndersenThermostat() : AndersenThermostat
• AndersenThermostatImpl() : AndersenThermostatImpl
• applyConstraints() : Context , ContextImpl
• applyVelocityConstraints() : Context , ContextImpl