  Context | A Context stores the complete state of a simulation |
| ContextImpl | This is the internal implementation of a Context |
 exception | |
  OpenMMException | This class is used for all exceptions thrown by OpenMM |
| Force | Force objects apply forces to the particles in a System, or alter their behavior in other ways |
| AmoebaAngleForce | This class implements an interaction between triplets of particles that varies with the angle between them |
| AmoebaBondForce | This class implements an interaction between pairs of particles that varies with the distance between them |
| AmoebaGeneralizedKirkwoodForce | This class implements an implicit solvation force using the generalized Kirkwood/Grycuk model |
| AmoebaInPlaneAngleForce | This class implements an interaction at trigonal centers corresponding to the projected in-plane angle bend energy between four particles |
| AmoebaMultipoleForce | This class implements the Amoeba multipole interaction |
| AmoebaOutOfPlaneBendForce | This class implements the Amoeba out-of-plane bend interaction |
| AmoebaPiTorsionForce | This class implements the Amoeba pi-torsion interaction |
| AmoebaStretchBendForce | This class implements the Amoeba stretch-bend interaction |
| AmoebaTorsionTorsionForce | This class implements the Amoeba torsion-torsion interaction |
| AmoebaVdwForce | This class implements a buffered 14-7 potential used to model van der Waals forces |
| AmoebaWcaDispersionForce | This class implements a nonbonded interaction between pairs of particles typically used along with AmoebaGeneralizedKirkwoodForce as part of an implicit solvent model |
| AndersenThermostat | This class uses the Andersen method to maintain constant temperature |
| CMAPTorsionForce | This class implements an interaction between pairs of dihedral angles |
| CMMotionRemover | This class prevents the center of mass of a System from drifting |
| CustomAngleForce | This class implements interactions between sets of three particles that depend on the angle between them |
| CustomBondForce | This class implements bonded interactions between pairs of particles |
| CustomCompoundBondForce | This class supports a wide variety of bonded interactions |
| CustomExternalForce | This class implements an "external" force on particles |
| CustomGBForce | This class implements complex, multiple stage nonbonded interactions between particles |
| CustomHbondForce | This class supports a wide variety of energy functions used to represent hydrogen bonding |
| CustomManyParticleForce | This class supports a wide variety of nonbonded N-particle interactions, where N is user specified |
| CustomNonbondedForce | This class implements nonbonded interactions between particles |
| CustomTorsionForce | This class implements interactions between sets of four particles that depend on the torsion angle between them |
| DrudeForce | This class implements forces that are specific to Drude oscillators |
| GBSAOBCForce | This class implements an implicit solvation force using the GBSA-OBC model |
| GBVIForce | This class implements an implicit solvation force using the GB/VI model |
| HarmonicAngleForce | This class implements an interaction between groups of three particles that varies harmonically with the angle between them |
| HarmonicBondForce | This class implements an interaction between pairs of particles that varies harmonically with the distance between them |
| MonteCarloAnisotropicBarostat | This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure |
| MonteCarloBarostat | This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure |
| MonteCarloMembraneBarostat | This is a Monte Carlo barostat designed specifically for membrane simulations |
| NonbondedForce | This class implements nonbonded interactions between particles, including a Coulomb force to represent electrostatics and a Lennard-Jones force to represent van der Waals interactions |
| PeriodicTorsionForce | This class implements an interaction between groups of four particles that varies periodically with the torsion angle between them |
| RBTorsionForce | This class implements an interaction between groups of four particles that varies with the torsion angle between them according to the Ryckaert-Bellemans potential |
| ForceImpl | A ForceImpl provides the internal implementation of a Force |
| AmoebaAngleForceImpl | This is the internal implementation of AmoebaAngleForce |
| AmoebaBondForceImpl | This is the internal implementation of AmoebaBondForce |
| AmoebaGeneralizedKirkwoodForceImpl | This is the internal implementation of AmoebaGeneralizedKirkwoodForce |
| AmoebaInPlaneAngleForceImpl | This is the internal implementation of AmoebaInPlaneAngleForce |
| AmoebaMultipoleForceImpl | This is the internal implementation of AmoebaMultipoleForce |
| AmoebaOutOfPlaneBendForceImpl | This is the internal implementation of AmoebaOutOfPlaneBendForce |
| AmoebaPiTorsionForceImpl | This is the internal implementation of AmoebaPiTorsionForce |
| AmoebaStretchBendForceImpl | This is the internal implementation of AmoebaStretchBendForce |
| AmoebaTorsionTorsionForceImpl | This is the internal implementation of AmoebaTorsionTorsionForce |
| AmoebaVdwForceImpl | This is the internal implementation of AmoebaVdwForce |
| AmoebaWcaDispersionForceImpl | This is the internal implementation of AmoebaWcaDispersionForce |
| AndersenThermostatImpl | This is the internal implementation of AndersenThermostat |
| CMAPTorsionForceImpl | This is the internal implementation of CMAPTorsionForce |
| CMMotionRemoverImpl | This is the internal implementation of CMMotionRemover |
| CustomAngleForceImpl | This is the internal implementation of CustomAngleForce |
| CustomBondForceImpl | This is the internal implementation of CustomBondForce |
| CustomCompoundBondForceImpl | This is the internal implementation of CustomCompoundBondForce |
| CustomExternalForceImpl | This is the internal implementation of CustomExternalForce |
| CustomGBForceImpl | This is the internal implementation of CustomGBForce |
| CustomHbondForceImpl | This is the internal implementation of CustomHbondForce |
| CustomManyParticleForceImpl | This is the internal implementation of CustomManyParticleForce |
| CustomNonbondedForceImpl | This is the internal implementation of CustomNonbondedForce |
| CustomTorsionForceImpl | This is the internal implementation of CustomTorsionForce |
| DrudeForceImpl | This is the internal implementation of DrudeForce |
| GBSAOBCForceImpl | This is the internal implementation of GBSAOBCForce |
| GBVIForceImpl | This is the internal implementation of GBVIForce |
| HarmonicAngleForceImpl | This is the internal implementation of HarmonicAngleForce |
| HarmonicBondForceImpl | This is the internal implementation of HarmonicBondForce |
| MonteCarloAnisotropicBarostatImpl | This is the internal implementation of MonteCarloAnisotropicBarostat |
| MonteCarloBarostatImpl | This is the internal implementation of MonteCarloBarostat |
| MonteCarloMembraneBarostatImpl | This is the internal implementation of MonteCarloMembraneBarostat |
| NonbondedForceImpl | This is the internal implementation of NonbondedForce |
| PeriodicTorsionForceImpl | This is the internal implementation of PeriodicTorsionForce |
| RBTorsionForceImpl | This is the internal implementation of RBTorsionForce |
| fvec4 | A four element vector of floats |
| fvec8 | An eight element vector of floats |
| Integrator | An Integrator defines a method for simulating a System by integrating the equations of motion |
| BrownianIntegrator | This is an Integrator which simulates a System using Brownian dynamics |
| CustomIntegrator | This is an Integrator that can be used to implemented arbitrary, user defined integration algorithms |
| DrudeLangevinIntegrator | This Integrator simulates systems that include Drude particles |
| DrudeSCFIntegrator | This is a leap-frog Verlet Integrator that simulates systems with Drude particles |
| LangevinIntegrator | This is an Integrator which simulates a System using Langevin dynamics |
| RPMDIntegrator | This is an Integrator which simulates a System using ring polymer molecular dynamics (RPMD) |
| VariableLangevinIntegrator | This is an error contolled, variable time step Integrator that simulates a System using Langevin dynamics |
| VariableVerletIntegrator | This is an error contolled, variable time step Integrator that simulates a System using the leap-frog Verlet algorithm |
| VerletIntegrator | This is an Integrator which simulates a System using the leap-frog Verlet algorithm |
| ivec4 | A four element vector of ints |
| ivec8 | An eight element vector of ints |
| Kernel | A Kernel encapsulates a particular implementation of a calculation that can be performed on the data in a Context |
| KernelFactory | A KernelFactory is an object that can create KernelImpls |
| KernelImpl | A KernelImpl defines the internal implementation of a Kernel object |
| LocalEnergyMinimizer | Given a Context, this class searches for a new set of particle positions that represent a local minimum of the potential energy |
| Platform | A Platform defines an implementation of all the kernels needed to perform some calculation |
| SplineFitter | SplineFitter provides routines for performing cubic spline interpolation |
| StateBuilder | |
| State | A State object records a snapshot of the current state of a simulation at a point in time |
| System | This class represents a molecular system |
| TabulatedFunction | A TabulatedFunction uses a set of tabulated values to define a mathematical function |
| Continuous1DFunction | This is a TabulatedFunction that computes a continuous one dimensional function |
| Continuous2DFunction | This is a TabulatedFunction that computes a continuous two dimensional function |
| Continuous3DFunction | This is a TabulatedFunction that computes a continuous three dimensional function |
| Discrete1DFunction | This is a TabulatedFunction that computes a discrete one dimensional function f(x) |
| Discrete2DFunction | This is a TabulatedFunction that computes a discrete two dimensional function f(x,y) |
| Discrete3DFunction | This is a TabulatedFunction that computes a discrete three dimensional function f(x,y,z) |
| Task | |
| ThreadPool | A ThreadPool creates a set of worker threads that can be used to execute tasks in parallel |
| Vec3 | This class represents a three component vector |
| VirtualSite | A VirtualSite describes the rules for computing a particle's position based on other particles |
| LocalCoordinatesSite | This is a VirtualSite that uses the locations of three other particles to compute a local coordinate system, then places the virtual site at a fixed location in that coordinate system |
| OutOfPlaneSite | This is a VirtualSite that computes the particle location based on three other particles' locations |
| ThreeParticleAverageSite | This is a VirtualSite that computes the particle location as a weighted average of three other particle's locations |
| TwoParticleAverageSite | This is a VirtualSite that computes the particle location as a weighted average of two other particle's locations |
| XmlSerializer | XmlSerializer is used for serializing objects as XML, and for reconstructing them again |
1.8.6 
