OpenMM
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Class List
Here are the classes, structs, unions and interfaces with brief descriptions:
[detail level 12345]
\Nsimtk
 \Nopenmm
  oNapp
  |oNamberinpcrdfile
  ||\CAmberInpcrdFileAmberInpcrdFile parses an AMBER inpcrd file and loads the data stored in it
  |oNamberprmtopfile
  ||\CAmberPrmtopFileAmberPrmtopFile parses an AMBER prmtop file and constructs a Topology and (optionally) an OpenMM System from it
  |oNdcdfile
  ||\CDCDFileDCDFile provides methods for creating DCD files
  |oNdcdreporter
  ||\CDCDReporterDCDReporter outputs a series of frames from a Simulation to a DCD file
  |oNelement
  ||\CElementAn Element represents a chemical element
  |oNforcefield
  ||\CForceFieldA ForceField constructs OpenMM System objects based on a Topology
  |oNgromacsgrofile
  ||\CGromacsGroFileGromacsGroFile parses a Gromacs .gro file and constructs a set of atom positions from it
  |oNgromacstopfile
  ||\CGromacsTopFileGromacsTopFile parses a Gromacs top file and constructs a Topology and (optionally) an OpenMM System from it
  |oNmodeller
  ||\CModellerModeller provides tools for editing molecular models, such as adding water or missing hydrogens
  |oNpdbfile
  ||\CPDBFilePDBFile parses a Protein Data Bank (PDB) file and constructs a Topology and a set of atom positions from it
  |oNpdbreporter
  ||\CPDBReporterPDBReporter outputs a series of frames from a Simulation to a PDB file
  |oNsimulation
  ||\CSimulationSimulation provides a simplified API for running simulations with OpenMM and reporting results
  |oNstatedatareporter
  ||\CStateDataReporterStateDataReporter outputs information about a simulation, such as energy and temperature, to a file
  |\Ntopology
  | oCTopologyTopology stores the topological information about a system
  | oCChainA Chain object represents a chain within a Topology
  | oCResidueA Residue object represents a residue within a Topology
  | \CAtomAn Atom object represents a residue within a Topology
  oNopenmm
  |oCStateA State object records a snapshot of the current state of a simulation at a point in time
  |oCForceForce objects apply forces to the particles in a System, or alter their behavior in other ways
  |oCAmoebaAngleForceThis class implements an interaction between triplets of particles that varies with the angle between them
  |oCAmoebaBondForceThis class implements an interaction between pairs of particles that varies with the distance between them
  |oCAmoebaGeneralizedKirkwoodForceThis class implements an implicit solvation force using the generalized Kirkwood/Grycuk model
  |oCAmoebaInPlaneAngleForceThis class implements an interaction at trigonal centers corresponding to the projected in-plane angle bend energy between four particles
  |oCAmoebaMultipoleForceThis class implements the Amoeba multipole interaction
  |oCAmoebaOutOfPlaneBendForceThis class implements the Amoeba out-of-plane bend interaction
  |oCAmoebaPiTorsionForceThis class implements the Amoeba pi-torsion interaction
  |oCAmoebaStretchBendForceThis class implements the Amoeba stretch-bend interaction
  |oCAmoebaTorsionTorsionForceThis class implements the Amoeba torsion-torsion interaction
  |oCAmoebaVdwForceThis class implements a buffered 14-7 potential used to model van der Waals forces
  |oCAmoebaWcaDispersionForceThis class implements a nonbonded interaction between pairs of particles typically used along with AmoebaGeneralizedKirkwoodForce as part of an implicit solvent model
  |oCAndersenThermostatThis class uses the Andersen method to maintain constant temperature
  |oCIntegratorAn Integrator defines a method for simulating a System by integrating the equations of motion
  |oCBrownianIntegratorThis is an Integrator which simulates a System using Brownian dynamics
  |oCCMAPTorsionForceThis class implements an interaction between pairs of dihedral angles
  |oCCMMotionRemoverThis class prevents the center of mass of a System from drifting
  |oCContextA Context stores the complete state of a simulation
  |oCCustomAngleForceThis class implements interactions between sets of three particles that depend on the angle between them
  |oCCustomBondForceThis class implements bonded interactions between pairs of particles
  |oCCustomCompoundBondForceThis class supports a wide variety of bonded interactions
  |oCCustomExternalForceThis class implements an "external" force on particles
  |oCCustomGBForceThis class implements complex, multiple stage nonbonded interactions between particles
  |oCCustomHbondForceThis class supports a wide variety of energy functions used to represent hydrogen bonding
  |oCCustomIntegratorThis is an Integrator that can be used to implemented arbitrary, user defined integration algorithms
  |oCCustomNonbondedForceThis class implements nonbonded interactions between particles
  |oCCustomTorsionForceThis class implements interactions between sets of four particles that depend on the torsion angle between them
  |oCGBSAOBCForceThis class implements an implicit solvation force using the GBSA-OBC model
  |oCGBVIForceThis class implements an implicit solvation force using the GB/VI model
  |oCHarmonicAngleForceThis class implements an interaction between groups of three particles that varies harmonically with the angle between them
  |oCHarmonicBondForceThis class implements an interaction between pairs of particles that varies harmonically with the distance between them
  |oCLangevinIntegratorThis is an Integrator which simulates a System using Langevin dynamics
  |oCLocalEnergyMinimizerGiven a Context, this class searches for a new set of particle positions that represent a local minimum of the potential energy
  |oCMonteCarloBarostatThis class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure
  |oCNonbondedForceThis class implements nonbonded interactions between particles, including a Coulomb force to represent electrostatics and a Lennard-Jones force to represent van der Waals interactions
  |oCOpenMMExceptionThis class is used for all exceptions thrown by OpenMM
  |oCVirtualSiteA VirtualSite describes the rules for computing a particle's position based on other particles
  |oCOutOfPlaneSiteThis is a VirtualSite that computes the particle location based on three other particles' locations
  |oCPeriodicTorsionForceThis class implements an interaction between groups of four particles that varies periodically with the torsion angle between them
  |oCPlatformA Platform defines an implementation of all the kernels needed to perform some calculation
  |oCRBTorsionForceThis class implements an interaction between groups of four particles that varies with the torsion angle between them according to the Ryckaert-Bellemans potential
  |oCRPMDIntegratorThis is an Integrator which simulates a System using ring polymer molecular dynamics (RPMD)
  |oCSystemThis class represents a molecular system
  |oCThreeParticleAverageSiteThis is a VirtualSite that computes the particle location as a weighted average of three other particle's locations
  |oCTwoParticleAverageSiteThis is a VirtualSite that computes the particle location as a weighted average of two other particle's locations
  |oCVariableLangevinIntegratorThis is an error contolled, variable time step Integrator that simulates a System using Langevin dynamics
  |oCVariableVerletIntegratorThis is an error contolled, variable time step Integrator that simulates a System using the leap-frog Verlet algorithm
  |oCVerletIntegratorThis is an Integrator which simulates a System using the leap-frog Verlet algorithm
  |\CXmlSerializerXmlSerializer is used for serializing objects as XML, and for reconstructing them again
  \Nvec3
   \CVec3Vec3 is a 3-element tuple that supports many math operations