- a -

• acceptor_list : CharmmPsfFile
• ANGLE_FORCE_GROUP : CharmmPsfFile
• angle_list : CharmmPsfFile
• angle_types : CharmmParameterSet
• atom_list : CharmmPsfFile
• atom_types_int : CharmmParameterSet
• atom_types_str : CharmmParameterSet
• atom_types_tuple : CharmmParameterSet
• atomNames : GromacsGroFile
• atomno : CharmmCrdFile
• attype : CharmmCrdFile

- b -

• Bisector : AmoebaMultipoleForce
• BOND_FORCE_GROUP : CharmmPsfFile
• bond_list : CharmmPsfFile
• bond_types : CharmmParameterSet
• box_vectors : CharmmPsfFile
• boxVectors : AmberInpcrdFile

- c -

• chain : Residue
• CMAP_FORCE_GROUP : CharmmPsfFile
• cmap_list : CharmmPsfFile
• cmap_types : CharmmParameterSet
• 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 : CustomGBForce , CustomHbondForce , CustomNonbondedForce , GBSAOBCForce , GBVIForce , NonbondedForce
• CutoffPeriodic : AmoebaVdwForce , CustomGBForce , CustomHbondForce , CustomNonbondedForce , GBSAOBCForce , GBVIForce , NonbondedForce

- d -

• DIHEDRAL_FORCE_GROUP : CharmmPsfFile
• dihedral_list : CharmmPsfFile
• dihedral_parameter_list : CharmmPsfFile
• dihedral_types : CharmmParameterSet
• Direct : AmoebaMultipoleForce
• donor_list : CharmmPsfFile

- e -

• element : Atom
• elements : AmberPrmtopFile , GromacsGroFile
• enrgstat : CharmmRstFile
• Ewald : NonbondedForce

- f -

• ff_version : CharmmRstFile
• file : AmberInpcrdFile
• flags : CharmmPsfFile

- g -

• GB_FORCE_GROUP : CharmmPsfFile
• group_list : CharmmPsfFile

- h -

• header : CharmmRstFile

- i -

• IMPROPER_FORCE_GROUP : CharmmPsfFile
• improper_list : CharmmPsfFile
• improper_types : CharmmParameterSet
• index : Atom , Chain , Residue
• integrator : Simulation

- j -

• jhstrt : CharmmRstFile

- l -

• LastAxisTypeIndex : AmoebaMultipoleForce

- m -

• Mutual : AmoebaMultipoleForce

- n -

• name : Atom , Residue
• natom : CharmmCrdFile , CharmmRstFile
• nbfix_types : CharmmParameterSet
• NoAxisType : AmoebaMultipoleForce
• NoCutoff : AmoebaMultipoleForce , AmoebaVdwForce , CustomGBForce , CustomHbondForce , CustomNonbondedForce , GBSAOBCForce , GBVIForce , NonbondedForce
• NONBONDED_FORCE_GROUP : CharmmPsfFile
• NoScaling : GBVIForce
• npriv : CharmmRstFile
• nsavc : CharmmRstFile
• nsavv : CharmmRstFile
• nstep : CharmmRstFile

- p -

• parametersets : CharmmParameterSet
• ParticlePair : CustomGBForce
• ParticlePairNoExclusions : CustomGBForce
• PME : AmoebaMultipoleForce , NonbondedForce
• PolarizationCovalent11 : AmoebaMultipoleForce
• PolarizationCovalent12 : AmoebaMultipoleForce
• PolarizationCovalent13 : AmoebaMultipoleForce
• PolarizationCovalent14 : AmoebaMultipoleForce
• positions : CharmmCrdFile , CharmmRstFile , CharmmPsfFile , DesmondDMSFile , GromacsGroFile , Modeller , PDBFile
• positionsold : CharmmRstFile
• provenance : DesmondDMSFile

- q -

• QuinticSpline : GBVIForce

- r -

• reporters : Simulation
• resid : CharmmCrdFile
• residue : Atom
• residue_list : CharmmPsfFile
• residueIds : GromacsGroFile
• residueNames : GromacsGroFile
• resname : CharmmCrdFile
• resno : CharmmCrdFile

- s -

• segid : CharmmCrdFile
• SingleParticle : CustomGBForce
• system : Simulation

- t -

• this : AmoebaAngleForce , AmoebaBondForce , AmoebaGeneralizedKirkwoodForce , AmoebaInPlaneAngleForce , AmoebaMultipoleForce , AmoebaOutOfPlaneBendForce , AmoebaPiTorsionForce , AmoebaStretchBendForce , AmoebaTorsionTorsionForce , AmoebaVdwForce , AmoebaWcaDispersionForce , AndersenThermostat , BrownianIntegrator , CMAPTorsionForce , CMMotionRemover , Context , Continuous1DFunction , Continuous2DFunction , Continuous3DFunction , CustomAngleForce , CustomBondForce , CustomCompoundBondForce , CustomExternalForce , CustomGBForce , CustomHbondForce , CustomIntegrator , CustomNonbondedForce , CustomTorsionForce , Discrete1DFunction , Discrete2DFunction , Discrete3DFunction , DrudeForce , DrudeLangevinIntegrator , DrudeSCFIntegrator , GBSAOBCForce , GBVIForce , HarmonicAngleForce , HarmonicBondForce , LangevinIntegrator , LocalCoordinatesSite , MonteCarloAnisotropicBarostat , MonteCarloBarostat , NonbondedForce , OpenMMException , OutOfPlaneSite , PeriodicTorsionForce , RBTorsionForce , RPMDIntegrator , System , ThreeParticleAverageSite , TwoParticleAverageSite , VariableLangevinIntegrator , VariableVerletIntegrator , VerletIntegrator
• ThreeFold : AmoebaMultipoleForce
• title : CharmmCrdFile , CharmmRstFile , CharmmPsfFile
• topology : AmberPrmtopFile , GromacsTopFile , Modeller , PDBFile , Simulation , Chain

- u -

• UpdateContextState : CustomIntegrator
• UREY_BRADLEY_FORCE_GROUP : CharmmPsfFile
• urey_bradley_list : CharmmPsfFile
• urey_bradley_types : CharmmParameterSet

- v -

• velocities : CharmmRstFile , CharmmPsfFile

- w -

• weighting : CharmmCrdFile

- z -

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