- a -

• atomic_number : Element

- b -

• Bisector : AmoebaMultipoleForce
• boxVectors : AmberInpcrdFile

- c -

• chain : Residue
• ComputeGlobal : CustomIntegrator
• ComputePerDof : CustomIntegrator
• ComputeSum : CustomIntegrator
• ConstrainPositions : CustomIntegrator
• ConstrainVelocities : CustomIntegrator
• context : Simulation
• Covalent12 : AmoebaMultipoleForce
• Covalent13 : AmoebaMultipoleForce
• Covalent14 : AmoebaMultipoleForce
• Covalent15 : AmoebaMultipoleForce
• CovalentEnd : AmoebaMultipoleForce
• currentStep : Simulation
• CutoffNonPeriodic : GBVIForce , CustomNonbondedForce , GBSAOBCForce , GBSAOBCSoftcoreForce , GBVISoftcoreForce , NonbondedForce , NonbondedSoftcoreForce , CustomGBForce , CustomHbondForce
• CutoffPeriodic : NonbondedSoftcoreForce , GBVIForce , CustomHbondForce , NonbondedForce , CustomGBForce , GBSAOBCSoftcoreForce , CustomNonbondedForce , GBVISoftcoreForce , GBSAOBCForce

- d -

• Direct : AmoebaMultipoleForce

- e -

• element : Atom
• Ewald : NonbondedForce

- i -

• index : Chain , Residue , Atom
• integrator : Simulation

- l -

• LastAxisTypeIndex : AmoebaMultipoleForce

- m -

• mass : Element
• Mutual : AmoebaMultipoleForce

- n -

• name : Element , Residue , Atom
• NoAxisType : AmoebaMultipoleForce
• NoCutoff : NonbondedForce , NonbondedSoftcoreForce , GBVIForce , GBSAOBCSoftcoreForce , CustomNonbondedForce , GBSAOBCForce , CustomHbondForce , GBVISoftcoreForce , AmoebaMultipoleForce , CustomGBForce
• NoScaling : GBVIForce , GBVISoftcoreForce

- p -

• ParticlePair : CustomGBForce
• ParticlePairNoExclusions : CustomGBForce
• PME : NonbondedForce , AmoebaMultipoleForce
• PolarizationCovalent11 : AmoebaMultipoleForce
• PolarizationCovalent12 : AmoebaMultipoleForce
• PolarizationCovalent13 : AmoebaMultipoleForce
• PolarizationCovalent14 : AmoebaMultipoleForce
• positions : PDBFile , AmberInpcrdFile , Modeller

- q -

• QuinticSpline : GBVIForce , GBVISoftcoreForce

- r -

• reporters : Simulation
• residue : Atom

- s -

• SingleParticle : CustomGBForce
• SOR : AmoebaMultipoleForce
• symbol : Element
• system : Simulation

- t -

• this : AmoebaGeneralizedKirkwoodForce , AmoebaHarmonicAngleForce , AmoebaHarmonicInPlaneAngleForce , AmoebaStretchBendForce , CMAPTorsionForce , HarmonicBondForce , LangevinIntegrator , VerletIntegrator , VariableVerletIntegrator , VariableLangevinIntegrator , TwoParticleAverageSite , ThreeParticleAverageSite , System , RPMDIntegrator , RBTorsionForce , PeriodicTorsionForce , OutOfPlaneSite , OpenMMException , NonbondedSoftcoreForce , CMMotionRemover , MonteCarloBarostat , NonbondedForce , AmoebaTorsionForce , HarmonicAngleForce , GBVISoftcoreForce , GBVIForce , GBSAOBCSoftcoreForce , GBSAOBCForce , CustomTorsionForce , CustomNonbondedForce , CustomIntegrator , CustomHbondForce , CustomGBForce , CustomExternalForce , CustomBondForce , Context , CustomAngleForce , AmoebaMultipoleForce , AmoebaTorsionTorsionForce , BrownianIntegrator , AndersenThermostat , AmoebaWcaDispersionForce , AmoebaVdwForce , AmoebaUreyBradleyForce , AmoebaHarmonicBondForce , AmoebaOutOfPlaneBendForce , AmoebaPiTorsionForce
• ThreeFold : AmoebaMultipoleForce
• topology : Modeller , PDBFile , AmberPrmtopFile , Simulation , Chain

- u -

• UpdateContextState : CustomIntegrator

- v -

• velocities : AmberInpcrdFile

- z -

• ZBisect : AmoebaMultipoleForce
• ZOnly : AmoebaMultipoleForce
• ZThenX : AmoebaMultipoleForce