# Library Layer¶

## Core Objects¶

`System` |
This class represents a molecular system. |

`Context` |
A Context stores the complete state of a simulation. |

`Platform` |
A Platform defines an implementation of all the kernels needed to perform some calculation. |

`State` |
A State object records a snapshot of the current state of a simulation at a point in time. |

## Forces¶

`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. |

`CustomCVForce` |
This class supports energy functions that depend on collective variables. |

`CustomCentroidBondForce` |
This class is similar to CustomCompoundBondForce, but instead of applying forces between individual particles, it applies them between the centers of groups 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. |

`Force` |
Force objects apply forces to the particles in a System, or alter their behavior in other ways. |

`GBSAOBCForce` |
This class implements an implicit solvation force using the GBSA-OBC model. |

`GayBerneForce` |
This class implements the Gay-Berne anisotropic potential. |

`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. |

`RMSDForce` |
This is a force whose energy equals the root mean squared deviation (RMSD) between the current coordinates and a reference structure. |

`RPMDMonteCarloBarostat` |
This class is very similar to MonteCarloBarostat, but it is specifically designed for use with RPMDIntegrator. |

## Integrators¶

`AMDForceGroupIntegrator` |
AMDForceGroupIntegrator implements a single boost aMD integration algorithm. |

`AMDIntegrator` |
AMDIntegrator implements the aMD integration algorithm. |

`BrownianIntegrator` |
This is an Integrator which simulates a System using Brownian dynamics. |

`CompoundIntegrator` |
This class allows you to use multiple integration algorithms within a single simulation, switching back and forth between them. |

`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. |

`DualAMDIntegrator` |
DualAMDIntegrator implements a dual boost aMD integration algorithm. |

`Integrator` |
An Integrator defines a method for simulating a System by integrating the equations of motion. |

`LangevinIntegrator` |
This is an Integrator which simulates a System using Langevin dynamics. |

`MTSIntegrator` |
MTSIntegrator implements the rRESPA multiple time step integration algorithm. |

`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. |

## Extras¶

`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). |

`LocalCoordinatesSite` |
This is a VirtualSite that uses the locations of several other particles to compute a local coordinate system, then places the virtual site at a fixed location in that coordinate system. |

`LocalEnergyMinimizer` |
Given a Context, this class searches for a new set of particle positions that represent a local minimum of the potential energy. |

`OutOfPlaneSite` |
This is a VirtualSite that computes the particle location based on three other particles’ locations. |

`SerializationNode` |
A SerializationNode stores information about an object during serialization or deserialization. |

`SerializationProxy` |
A SerializationProxy is an object that knows how to serialize and deserialize objects of a particular type. |

`TabulatedFunction` |
A TabulatedFunction uses a set of tabulated values to define a mathematical function. |

`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. |

`Vec3` |
Vec3 is a 3-element tuple that supports many math operations. |

`VirtualSite` |
A VirtualSite describes the rules for computing a particle’s position based on other particles. |

`XmlSerializer` |
XmlSerializer is used for serializing objects as XML, and for reconstructing them again. |