| ▼Nsimtk | |
| ▼Nopenmm | |
| ▼Namd | |
| CAMDForceGroupIntegrator | AMDForceGroupIntegrator implements a single boost aMD integration algorithm |
| CAMDIntegrator | AMDIntegrator implements the aMD integration algorithm |
| CDualAMDIntegrator | DualAMDIntegrator implements a dual boost aMD integration algorithm |
| ▼Napp | |
| ►Namberinpcrdfile | |
| CAmberInpcrdFile | AmberInpcrdFile parses an AMBER inpcrd file and loads the data stored in it |
| ►Namberprmtopfile | |
| CAmberPrmtopFile | AmberPrmtopFile parses an AMBER prmtop file and constructs a Topology and (optionally) an OpenMM System from it |
| CGBn | |
| CGBn2 | |
| CHCT | |
| COBC1 | |
| COBC2 | |
| ►Ncharmmcrdfiles | |
| CCharmmCrdFile | Reads and parses a CHARMM coordinate file (.crd) into its components, namely the coordinates, CHARMM atom types, resid, resname, etc |
| CCharmmRstFile | Reads and parses data, velocities and coordinates from a CHARMM restart file (.rst) of file name 'fname' into class attributes |
| ►Ncharmmparameterset | |
| CCharmmParameterSet | Stores a parameter set defined by CHARMM files |
| ►Ncharmmpsffile | |
| CCharmmPsfFile | A chemical structure instantiated from CHARMM files |
| ►Ncheckpointreporter | |
| CCheckpointReporter | CheckpointReporter saves periodic checkpoints of a simulation |
| ►Ndcdfile | |
| CDCDFile | DCDFile provides methods for creating DCD files |
| ►Ndcdreporter | |
| CDCDReporter | DCDReporter outputs a series of frames from a Simulation to a DCD file |
| ►Ndesmonddmsfile | |
| CDesmondDMSFile | DesmondDMSFile parses a Desmond DMS (desmond molecular system) and constructs a topology and (optionally) an OpenMM System from it |
| ►Nelement | |
| CElement | An Element represents a chemical element |
| ►Nforcefield | |
| CAllBonds | |
| CCutoffNonPeriodic | |
| CCutoffPeriodic | |
| CEwald | |
| CForceField | A ForceField constructs OpenMM System objects based on a Topology |
| CHAngles | |
| CHBonds | |
| CNoCutoff | |
| CPME | |
| ►Ngromacsgrofile | |
| CGromacsGroFile | GromacsGroFile parses a Gromacs .gro file and constructs a set of atom positions from it |
| ►Ngromacstopfile | |
| CGromacsTopFile | GromacsTopFile parses a Gromacs top file and constructs a Topology and (optionally) an OpenMM System from it |
| ►Nmodeller | |
| CModeller | Modeller provides tools for editing molecular models, such as adding water or missing hydrogens |
| ►Npdbfile | |
| CPDBFile | PDBFile parses a Protein Data Bank (PDB) file and constructs a Topology and a set of atom positions from it |
| ►Npdbreporter | |
| CPDBReporter | PDBReporter outputs a series of frames from a Simulation to a PDB file |
| ►Npdbxfile | |
| CPDBxFile | PDBxFile parses a PDBx/mmCIF file and constructs a Topology and a set of atom positions from it |
| ►Nsimulation | |
| CSimulation | Simulation provides a simplified API for running simulations with OpenMM and reporting results |
| ►Nstatedatareporter | |
| CStateDataReporter | StateDataReporter outputs information about a simulation, such as energy and temperature, to a file |
| ►Ntopology | |
| CAtom | An Atom object represents a residue within a Topology |
| CChain | A Chain object represents a chain within a Topology |
| CResidue | A Residue object represents a residue within a Topology |
| CTopology | Topology stores the topological information about a system |
| ▼Nmtsintegrator | |
| CMTSIntegrator | MTSIntegrator implements the rRESPA multiple time step integration algorithm |
| ▼Nopenmm | |
| CAmoebaAngleForce | This class implements an interaction between triplets of particles that varies with the angle between them |
| CAmoebaBondForce | This class implements an interaction between pairs of particles that varies with the distance between them |
| CAmoebaGeneralizedKirkwoodForce | This class implements an implicit solvation force using the generalized Kirkwood/Grycuk model |
| CAmoebaInPlaneAngleForce | This class implements an interaction at trigonal centers corresponding to the projected in-plane angle bend energy between four particles |
| CAmoebaMultipoleForce | This class implements the Amoeba multipole interaction |
| CAmoebaOutOfPlaneBendForce | This class implements the Amoeba out-of-plane bend interaction |
| CAmoebaPiTorsionForce | This class implements the Amoeba pi-torsion interaction |
| CAmoebaStretchBendForce | This class implements the Amoeba stretch-bend interaction |
| CAmoebaTorsionTorsionForce | This class implements the Amoeba torsion-torsion interaction |
| CAmoebaVdwForce | This class implements a buffered 14-7 potential used to model van der Waals forces |
| CAmoebaWcaDispersionForce | This class implements a nonbonded interaction between pairs of particles typically used along with AmoebaGeneralizedKirkwoodForce as part of an implicit solvent model |
| CAndersenThermostat | This class uses the Andersen method to maintain constant temperature |
| CBrownianIntegrator | This is an Integrator which simulates a System using Brownian dynamics |
| CCMAPTorsionForce | This class implements an interaction between pairs of dihedral angles |
| CCMMotionRemover | This class prevents the center of mass of a System from drifting |
| CContext | A Context stores the complete state of a simulation |
| CContinuous1DFunction | This is a TabulatedFunction that computes a continuous one dimensional function |
| CContinuous2DFunction | This is a TabulatedFunction that computes a continuous two dimensional function |
| CContinuous3DFunction | This is a TabulatedFunction that computes a continuous three dimensional function |
| CCustomAngleForce | This class implements interactions between sets of three particles that depend on the angle between them |
| CCustomBondForce | This class implements bonded interactions between pairs of particles |
| CCustomCompoundBondForce | This class supports a wide variety of bonded interactions |
| CCustomExternalForce | This class implements an "external" force on particles |
| CCustomGBForce | This class implements complex, multiple stage nonbonded interactions between particles |
| CCustomHbondForce | This class supports a wide variety of energy functions used to represent hydrogen bonding |
| CCustomIntegrator | This is an Integrator that can be used to implemented arbitrary, user defined integration algorithms |
| CCustomManyParticleForce | This class supports a wide variety of nonbonded N-particle interactions, where N is user specified |
| CCustomNonbondedForce | This class implements nonbonded interactions between particles |
| CCustomTorsionForce | This class implements interactions between sets of four particles that depend on the torsion angle between them |
| CDiscrete1DFunction | This is a TabulatedFunction that computes a discrete one dimensional function f(x) |
| CDiscrete2DFunction | This is a TabulatedFunction that computes a discrete two dimensional function f(x,y) |
| CDiscrete3DFunction | This is a TabulatedFunction that computes a discrete three dimensional function f(x,y,z) |
| CDrudeForce | This class implements forces that are specific to Drude oscillators |
| CDrudeLangevinIntegrator | This Integrator simulates systems that include Drude particles |
| CDrudeSCFIntegrator | This is a leap-frog Verlet Integrator that simulates systems with Drude particles |
| CForce | Force objects apply forces to the particles in a System, or alter their behavior in other ways |
| CGBSAOBCForce | This class implements an implicit solvation force using the GBSA-OBC model |
| CGBVIForce | This class implements an implicit solvation force using the GB/VI model |
| CHarmonicAngleForce | This class implements an interaction between groups of three particles that varies harmonically with the angle between them |
| CHarmonicBondForce | This class implements an interaction between pairs of particles that varies harmonically with the distance between them |
| CIntegrator | An Integrator defines a method for simulating a System by integrating the equations of motion |
| CLangevinIntegrator | This is an Integrator which simulates a System using Langevin dynamics |
| CLocalCoordinatesSite | 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 |
| CLocalEnergyMinimizer | Given a Context, this class searches for a new set of particle positions that represent a local minimum of the potential energy |
| CMonteCarloAnisotropicBarostat | This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure |
| CMonteCarloBarostat | This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure |
| CMonteCarloMembraneBarostat | This is a Monte Carlo barostat designed specifically for membrane simulations |
| CNonbondedForce | 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 |
| COpenMMException | This class is used for all exceptions thrown by OpenMM |
| COutOfPlaneSite | This is a VirtualSite that computes the particle location based on three other particles' locations |
| CPeriodicTorsionForce | This class implements an interaction between groups of four particles that varies periodically with the torsion angle between them |
| CPlatform | A Platform defines an implementation of all the kernels needed to perform some calculation |
| CRBTorsionForce | This class implements an interaction between groups of four particles that varies with the torsion angle between them according to the Ryckaert-Bellemans potential |
| CRPMDIntegrator | This is an Integrator which simulates a System using ring polymer molecular dynamics (RPMD) |
| CRPMDMonteCarloBarostat | This class is very similar to MonteCarloBarostat, but it is specifically designed for use with RPMDIntegrator |
| CState | A State object records a snapshot of the current state of a simulation at a point in time |
| CSystem | This class represents a molecular system |
| CTabulatedFunction | A TabulatedFunction uses a set of tabulated values to define a mathematical function |
| CThreeParticleAverageSite | This is a VirtualSite that computes the particle location as a weighted average of three other particle's locations |
| CTwoParticleAverageSite | This is a VirtualSite that computes the particle location as a weighted average of two other particle's locations |
| CVariableLangevinIntegrator | This is an error contolled, variable time step Integrator that simulates a System using Langevin dynamics |
| CVariableVerletIntegrator | This is an error contolled, variable time step Integrator that simulates a System using the leap-frog Verlet algorithm |
| CVerletIntegrator | This is an Integrator which simulates a System using the leap-frog Verlet algorithm |
| CVirtualSite | A VirtualSite describes the rules for computing a particle's position based on other particles |
| CXmlSerializer | XmlSerializer is used for serializing objects as XML, and for reconstructing them again |
| ▼Nvec3 | |
| CVec3 | Vec3 is a 3-element tuple that supports many math operations |
1.8.8 
