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Class Hierarchy
This inheritance list is sorted roughly, but not completely, alphabetically:

Context | A Context stores the complete state of a simulation
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
RPMDMonteCarloBarostat | This class is very similar to MonteCarloBarostat, but it is specifically designed for use with RPMDIntegrator
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
LocalEnergyMinimizer | Given a Context, this class searches for a new set of particle positions that represent a local minimum of the potential energy
object |
AmberInpcrdFile | AmberInpcrdFile parses an AMBER inpcrd file and loads the data stored in it
AmberPrmtopFile | AmberPrmtopFile parses an AMBER prmtop file and constructs a Topology and (optionally) an OpenMM System from it
GBn |
GBn2 |
HCT |
OBC1 |
OBC2 |
CharmmCrdFile | Reads and parses a CHARMM coordinate file (.crd) into its components, namely the coordinates, CHARMM atom types, resid, resname, etc
CharmmRstFile | Reads and parses data, velocities and coordinates from a CHARMM restart file (.rst) of file name 'fname' into class attributes
CharmmParameterSet | Stores a parameter set defined by CHARMM files
CharmmPsfFile | A chemical structure instantiated from CHARMM files
CheckpointReporter | CheckpointReporter saves periodic checkpoints of a simulation
DCDFile | DCDFile provides methods for creating DCD files
DCDReporter | DCDReporter outputs a series of frames from a Simulation to a DCD file
DesmondDMSFile | DesmondDMSFile parses a Desmond DMS (desmond molecular system) and constructs a topology and (optionally) an OpenMM System from it
Element | An Element represents a chemical element
AllBonds |
CutoffNonPeriodic |
CutoffPeriodic |
Ewald |
ForceField | A ForceField constructs OpenMM System objects based on a Topology
HAngles |
HBonds |
NoCutoff |
PME |
GromacsGroFile | GromacsGroFile parses a Gromacs .gro file and constructs a set of atom positions from it
GromacsTopFile | GromacsTopFile parses a Gromacs top file and constructs a Topology and (optionally) an OpenMM System from it
Modeller | Modeller provides tools for editing molecular models, such as adding water or missing hydrogens
PDBFile | PDBFile parses a Protein Data Bank (PDB) file and constructs a Topology and a set of atom positions from it
PDBReporter | PDBReporter outputs a series of frames from a Simulation to a PDB file
PDBxFile | PDBxFile parses a PDBx/mmCIF file and constructs a Topology and a set of atom positions from it
Simulation | Simulation provides a simplified API for running simulations with OpenMM and reporting results
StateDataReporter | StateDataReporter outputs information about a simulation, such as energy and temperature, to a file
Atom | An Atom object represents a residue within a Topology
Chain | A Chain object represents a chain within a Topology
Residue | A Residue object represents a residue within a Topology
Topology | Topology stores the topological information about a system
OpenMMException | This class is used for all exceptions thrown by OpenMM
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
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)
tuple |
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
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
CustomIntegrator |
AMDForceGroupIntegrator | AMDForceGroupIntegrator implements a single boost aMD integration algorithm
AMDIntegrator | AMDIntegrator implements the aMD integration algorithm
DualAMDIntegrator | DualAMDIntegrator implements a dual boost aMD integration algorithm
MTSIntegrator | MTSIntegrator implements the rRESPA multiple time step integration algorithm