OpenMM
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Class Hierarchy
This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 12]
oCContextA Context stores the complete state of a simulation
oCElementAn Element represents a chemical element
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
|oCCMAPTorsionForceThis class implements an interaction between pairs of dihedral angles
|oCCMMotionRemoverThis class prevents the center of mass of a System from drifting
|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
|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
|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
|oCPeriodicTorsionForceThis class implements an interaction between groups of four particles that varies periodically with the torsion angle between them
|\CRBTorsionForceThis class implements an interaction between groups of four particles that varies with the torsion angle between them according to the Ryckaert-Bellemans potential
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
|oCCustomIntegratorThis is an Integrator that can be used to implemented arbitrary, user defined integration algorithms
|oCLangevinIntegratorThis is an Integrator which simulates a System using Langevin dynamics
|oCRPMDIntegratorThis is an Integrator which simulates a System using ring polymer molecular dynamics (RPMD)
|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
|\CVerletIntegratorThis is an Integrator which simulates a System using the leap-frog Verlet algorithm
oCLocalEnergyMinimizerGiven a Context, this class searches for a new set of particle positions that represent a local minimum of the potential energy
oCobject
|oCAmberInpcrdFileAmberInpcrdFile parses an AMBER inpcrd file and loads the data stored in it
|oCAmberPrmtopFileAmberPrmtopFile parses an AMBER prmtop file and constructs a Topology and (optionally) an OpenMM System from it
|oCDCDFileDCDFile provides methods for creating DCD files
|oCDCDReporterDCDReporter outputs a series of frames from a Simulation to a DCD file
|oCForceFieldA ForceField constructs OpenMM System objects based on a Topology
|oCGromacsGroFileGromacsGroFile parses a Gromacs .gro file and constructs a set of atom positions from it
|oCGromacsTopFileGromacsTopFile parses a Gromacs top file and constructs a Topology and (optionally) an OpenMM System from it
|oCModellerModeller provides tools for editing molecular models, such as adding water or missing hydrogens
|oCPDBFilePDBFile parses a Protein Data Bank (PDB) file and constructs a Topology and a set of atom positions from it
|oCPDBReporterPDBReporter outputs a series of frames from a Simulation to a PDB file
|oCSimulationSimulation provides a simplified API for running simulations with OpenMM and reporting results
|oCStateDataReporterStateDataReporter outputs information about a simulation, such as energy and temperature, to a file
|oCAtomAn Atom object represents a residue within a Topology
|oCChainA Chain object represents a chain within a Topology
|oCResidueA Residue object represents a residue within a Topology
|\CTopologyTopology stores the topological information about a system
oCOpenMMExceptionThis class is used for all exceptions thrown by OpenMM
oCPlatformA Platform defines an implementation of all the kernels needed to perform some calculation
oCStateA State object records a snapshot of the current state of a simulation at a point in time
oCSystemThis class represents a molecular system
oCtuple
|\CVec3Vec3 is a 3-element tuple that supports many math operations
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
|oCThreeParticleAverageSiteThis is a VirtualSite that computes the particle location as a weighted average of three other particle's locations
|\CTwoParticleAverageSiteThis is a VirtualSite that computes the particle location as a weighted average of two other particle's locations
\CXmlSerializerXmlSerializer is used for serializing objects as XML, and for reconstructing them again