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.
`HippoNonbondedForce`	This class implements all nonbonded interactions in the HIPPO force field: electrostatics, induction, charge transfer, dispersion, and repulsion.
`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.