- a -

• atomic_number : Element
• atomNames : GromacsGroFile

- 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 : CustomNonbondedForce , GBSAOBCForce , GBVIForce , NonbondedForce , CustomHbondForce , CustomGBForce
• CutoffPeriodic : AmoebaVdwForce , GBSAOBCForce , NonbondedForce , GBVIForce , CustomGBForce , CustomHbondForce , CustomNonbondedForce

- d -

• Direct : AmoebaMultipoleForce

- e -

• element : Atom
• elements : GromacsGroFile
• 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 : GBSAOBCForce , CustomNonbondedForce , GBVIForce , CustomGBForce , AmoebaVdwForce , AmoebaMultipoleForce , CustomHbondForce , NonbondedForce
• NoScaling : GBVIForce

- p -

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

- q -

• QuinticSpline : GBVIForce

- r -

• reporters : Simulation
• residue : Atom
• residueIds : GromacsGroFile
• residueNames : GromacsGroFile

- s -

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

- t -

• this : AmoebaAngleForce , AmoebaBondForce , AmoebaInPlaneAngleForce , AmoebaStretchBendForce , Context , NonbondedForce , OpenMMException , CustomAngleForce , VerletIntegrator , VariableVerletIntegrator , VariableLangevinIntegrator , TwoParticleAverageSite , ThreeParticleAverageSite , System , RPMDIntegrator , RBTorsionForce , OutOfPlaneSite , PeriodicTorsionForce , AmoebaTorsionTorsionForce , CustomBondForce , MonteCarloBarostat , LangevinIntegrator , HarmonicBondForce , HarmonicAngleForce , GBVIForce , GBSAOBCForce , CustomTorsionForce , CustomNonbondedForce , CustomIntegrator , CustomHbondForce , CustomGBForce , CustomExternalForce , CustomCompoundBondForce , AmoebaMultipoleForce , AmoebaVdwForce , AmoebaWcaDispersionForce , CMMotionRemover , CMAPTorsionForce , BrownianIntegrator , AndersenThermostat , AmoebaGeneralizedKirkwoodForce , AmoebaOutOfPlaneBendForce , AmoebaPiTorsionForce
• ThreeFold : AmoebaMultipoleForce
• topology : Modeller , GromacsTopFile , AmberPrmtopFile , PDBFile , Simulation , Chain

- u -

• UpdateContextState : CustomIntegrator

- v -

• velocities : AmberInpcrdFile

- z -

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