▼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 |