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.
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.
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 three 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.