OpenMM

- Main Page
- Related Pages
- Classes

- Class List
- Class Hierarchy
- Class Members

All Classes Namespaces Functions Variables Pages
Class List
Here are the classes, structs, unions and interfaces with brief descriptions:
[detail level 1 2 3 4 5]

▼N simtk |
▼N openmm |
▼N amd |
C AMDForceGroupIntegrator | AMDForceGroupIntegrator implements a single boost aMD integration algorithm
C AMDIntegrator | AMDIntegrator implements the aMD integration algorithm
C DualAMDIntegrator | DualAMDIntegrator implements a dual boost aMD integration algorithm
▼N app |
►N amberinpcrdfile |
C AmberInpcrdFile | AmberInpcrdFile parses an AMBER inpcrd file and loads the data stored in it
►N amberprmtopfile |
C AmberPrmtopFile | AmberPrmtopFile parses an AMBER prmtop file and constructs a Topology and (optionally) an OpenMM System from it
C GBn |
C GBn2 |
C HCT |
C OBC1 |
C OBC2 |
►N charmmcrdfiles |
C CharmmCrdFile | Reads and parses a CHARMM coordinate file (.crd) into its components, namely the coordinates, CHARMM atom types, resid, resname, etc
C CharmmRstFile | Reads and parses data, velocities and coordinates from a CHARMM restart file (.rst) of file name 'fname' into class attributes
►N charmmparameterset |
C CharmmParameterSet | Stores a parameter set defined by CHARMM files
►N charmmpsffile |
C CharmmPsfFile | A chemical structure instantiated from CHARMM files
►N checkpointreporter |
C CheckpointReporter | CheckpointReporter saves periodic checkpoints of a simulation
►N dcdfile |
C DCDFile | DCDFile provides methods for creating DCD files
►N dcdreporter |
C DCDReporter | DCDReporter outputs a series of frames from a Simulation to a DCD file
►N desmonddmsfile |
C DesmondDMSFile | DesmondDMSFile parses a Desmond DMS (desmond molecular system) and constructs a topology and (optionally) an OpenMM System from it
►N element |
C Element | An Element represents a chemical element
►N forcefield |
C AllBonds |
C CutoffNonPeriodic |
C CutoffPeriodic |
C Ewald |
C ForceField | A ForceField constructs OpenMM System objects based on a Topology
C HAngles |
C HBonds |
C NoCutoff |
C PME |
►N gromacsgrofile |
C GromacsGroFile | GromacsGroFile parses a Gromacs .gro file and constructs a set of atom positions from it
►N gromacstopfile |
C GromacsTopFile | GromacsTopFile parses a Gromacs top file and constructs a Topology and (optionally) an OpenMM System from it
►N modeller |
C Modeller | Modeller provides tools for editing molecular models, such as adding water or missing hydrogens
►N pdbfile |
C PDBFile | PDBFile parses a Protein Data Bank (PDB) file and constructs a Topology and a set of atom positions from it
►N pdbreporter |
C PDBReporter | PDBReporter outputs a series of frames from a Simulation to a PDB file
►N pdbxfile |
C PDBxFile | PDBxFile parses a PDBx/mmCIF file and constructs a Topology and a set of atom positions from it
►N simulation |
C Simulation | Simulation provides a simplified API for running simulations with OpenMM and reporting results
►N statedatareporter |
C StateDataReporter | StateDataReporter outputs information about a simulation, such as energy and temperature, to a file
►N topology |
C Atom | An Atom object represents a residue within a Topology
C Chain | A Chain object represents a chain within a Topology
C Residue | A Residue object represents a residue within a Topology
C Topology | Topology stores the topological information about a system
▼N mtsintegrator |
C MTSIntegrator | MTSIntegrator implements the rRESPA multiple time step integration algorithm
▼N openmm |
C AmoebaAngleForce | This class implements an interaction between triplets of particles that varies with the angle between them
C AmoebaBondForce | This class implements an interaction between pairs of particles that varies with the distance between them
C AmoebaGeneralizedKirkwoodForce | This class implements an implicit solvation force using the generalized Kirkwood/Grycuk model
C AmoebaInPlaneAngleForce | This class implements an interaction at trigonal centers corresponding to the projected in-plane angle bend energy between four particles
C AmoebaMultipoleForce | This class implements the Amoeba multipole interaction
C AmoebaOutOfPlaneBendForce | This class implements the Amoeba out-of-plane bend interaction
C AmoebaPiTorsionForce | This class implements the Amoeba pi-torsion interaction
C AmoebaStretchBendForce | This class implements the Amoeba stretch-bend interaction
C AmoebaTorsionTorsionForce | This class implements the Amoeba torsion-torsion interaction
C AmoebaVdwForce | This class implements a buffered 14-7 potential used to model van der Waals forces
C AmoebaWcaDispersionForce | This class implements a nonbonded interaction between pairs of particles typically used along with AmoebaGeneralizedKirkwoodForce as part of an implicit solvent model
C AndersenThermostat | This class uses the Andersen method to maintain constant temperature
C BrownianIntegrator | This is an Integrator which simulates a System using Brownian dynamics
C CMAPTorsionForce | This class implements an interaction between pairs of dihedral angles
C CMMotionRemover | This class prevents the center of mass of a System from drifting
C Context | A Context stores the complete state of a simulation
C Continuous1DFunction | This is a TabulatedFunction that computes a continuous one dimensional function
C Continuous2DFunction | This is a TabulatedFunction that computes a continuous two dimensional function
C Continuous3DFunction | This is a TabulatedFunction that computes a continuous three dimensional function
C CustomAngleForce | This class implements interactions between sets of three particles that depend on the angle between them
C CustomBondForce | This class implements bonded interactions between pairs of particles
C CustomCompoundBondForce | This class supports a wide variety of bonded interactions
C CustomExternalForce | This class implements an "external" force on particles
C CustomGBForce | This class implements complex, multiple stage nonbonded interactions between particles
C CustomHbondForce | This class supports a wide variety of energy functions used to represent hydrogen bonding
C CustomIntegrator | This is an Integrator that can be used to implemented arbitrary, user defined integration algorithms
C CustomManyParticleForce | This class supports a wide variety of nonbonded N-particle interactions, where N is user specified
C CustomNonbondedForce | This class implements nonbonded interactions between particles
C CustomTorsionForce | This class implements interactions between sets of four particles that depend on the torsion angle between them
C Discrete1DFunction | This is a TabulatedFunction that computes a discrete one dimensional function f(x)
C Discrete2DFunction | This is a TabulatedFunction that computes a discrete two dimensional function f(x,y)
C Discrete3DFunction | This is a TabulatedFunction that computes a discrete three dimensional function f(x,y,z)
C DrudeForce | This class implements forces that are specific to Drude oscillators
C DrudeLangevinIntegrator | This Integrator simulates systems that include Drude particles
C DrudeSCFIntegrator | This is a leap-frog Verlet Integrator that simulates systems with Drude particles
C Force | Force objects apply forces to the particles in a System, or alter their behavior in other ways
C GBSAOBCForce | This class implements an implicit solvation force using the GBSA-OBC model
C GBVIForce | This class implements an implicit solvation force using the GB/VI model
C HarmonicAngleForce | This class implements an interaction between groups of three particles that varies harmonically with the angle between them
C HarmonicBondForce | This class implements an interaction between pairs of particles that varies harmonically with the distance between them
C Integrator | An Integrator defines a method for simulating a System by integrating the equations of motion
C LangevinIntegrator | This is an Integrator which simulates a System using Langevin dynamics
C 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
C LocalEnergyMinimizer | Given a Context, this class searches for a new set of particle positions that represent a local minimum of the potential energy
C MonteCarloAnisotropicBarostat | This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure
C MonteCarloBarostat | This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure
C MonteCarloMembraneBarostat | This is a Monte Carlo barostat designed specifically for membrane simulations
C 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
C OpenMMException | This class is used for all exceptions thrown by OpenMM
C OutOfPlaneSite | This is a VirtualSite that computes the particle location based on three other particles' locations
C PeriodicTorsionForce | This class implements an interaction between groups of four particles that varies periodically with the torsion angle between them
C Platform | A Platform defines an implementation of all the kernels needed to perform some calculation
C 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
C RPMDIntegrator | This is an Integrator which simulates a System using ring polymer molecular dynamics (RPMD)
C RPMDMonteCarloBarostat | This class is very similar to MonteCarloBarostat, but it is specifically designed for use with RPMDIntegrator
C State | A State object records a snapshot of the current state of a simulation at a point in time
C System | This class represents a molecular system
C TabulatedFunction | A TabulatedFunction uses a set of tabulated values to define a mathematical function
C ThreeParticleAverageSite | This is a VirtualSite that computes the particle location as a weighted average of three other particle's locations
C TwoParticleAverageSite | This is a VirtualSite that computes the particle location as a weighted average of two other particle's locations
C VariableLangevinIntegrator | This is an error contolled, variable time step Integrator that simulates a System using Langevin dynamics
C VariableVerletIntegrator | This is an error contolled, variable time step Integrator that simulates a System using the leap-frog Verlet algorithm
C VerletIntegrator | This is an Integrator which simulates a System using the leap-frog Verlet algorithm
C VirtualSite | A VirtualSite describes the rules for computing a particle's position based on other particles
C XmlSerializer | XmlSerializer is used for serializing objects as XML, and for reconstructing them again
▼N vec3 |
C Vec3 | Vec3 is a 3-element tuple that supports many math operations