![\](ftv2mlastnode.png) simtk | |
![](ftv2blank.png) ![\](ftv2mlastnode.png) openmm | |
![](ftv2blank.png) ![](ftv2blank.png) ![o](ftv2mnode.png) app | |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2mnode.png) amberinpcrdfile | |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) AmberInpcrdFile | AmberInpcrdFile parses an AMBER inpcrd file and loads the data stored in it |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2mnode.png) amberprmtopfile | |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) AmberPrmtopFile | AmberPrmtopFile parses an AMBER prmtop file and constructs a Topology and (optionally) an OpenMM System from it |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2mnode.png) dcdfile | |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) DCDFile | DCDFile provides methods for creating DCD files |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2mnode.png) dcdreporter | |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) DCDReporter | DCDReporter outputs a series of frames from a Simulation to a DCD file |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2mnode.png) element | |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Element | An Element represents a chemical element |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2mnode.png) forcefield | |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) ForceField | A ForceField constructs OpenMM System objects based on a Topology |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2mnode.png) gromacsgrofile | |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) GromacsGroFile | GromacsGroFile parses a Gromacs .gro file and constructs a set of atom positions from it |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2mnode.png) gromacstopfile | |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) GromacsTopFile | GromacsTopFile parses a Gromacs top file and constructs a Topology and (optionally) an OpenMM System from it |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2mnode.png) modeller | |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Modeller | Modeller provides tools for editing molecular models, such as adding water or missing hydrogens |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2mnode.png) pdbfile | |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) PDBFile | PDBFile parses a Protein Data Bank (PDB) file and constructs a Topology and a set of atom positions from it |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2mnode.png) pdbreporter | |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) PDBReporter | PDBReporter outputs a series of frames from a Simulation to a PDB file |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2mnode.png) simulation | |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Simulation | Simulation provides a simplified API for running simulations with OpenMM and reporting results |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2mnode.png) statedatareporter | |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) StateDataReporter | StateDataReporter outputs information about a simulation, such as energy and temperature, to a file |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![\](ftv2mlastnode.png) topology | |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![](ftv2blank.png) ![o](ftv2node.png) Topology | Topology stores the topological information about a system |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![](ftv2blank.png) ![o](ftv2node.png) Chain | A Chain object represents a chain within a Topology |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![](ftv2blank.png) ![o](ftv2node.png) Residue | A Residue object represents a residue within a Topology |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![](ftv2blank.png) ![\](ftv2lastnode.png) Atom | An Atom object represents a residue within a Topology |
![](ftv2blank.png) ![](ftv2blank.png) ![o](ftv2mnode.png) openmm | |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) State | A State object records a snapshot of the current state of a simulation at a point in time |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) Force | Force objects apply forces to the particles in a System, or alter their behavior in other ways |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) AmoebaAngleForce | This class implements an interaction between triplets of particles that varies with the angle between them |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) AmoebaBondForce | This class implements an interaction between pairs of particles that varies with the distance between them |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) AmoebaGeneralizedKirkwoodForce | This class implements an implicit solvation force using the generalized Kirkwood/Grycuk model |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) AmoebaInPlaneAngleForce | This class implements an interaction at trigonal centers corresponding to the projected in-plane angle bend energy between four particles |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) AmoebaMultipoleForce | This class implements the Amoeba multipole interaction |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) AmoebaOutOfPlaneBendForce | This class implements the Amoeba out-of-plane bend interaction |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) AmoebaPiTorsionForce | This class implements the Amoeba pi-torsion interaction |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) AmoebaStretchBendForce | This class implements the Amoeba stretch-bend interaction |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) AmoebaTorsionTorsionForce | This class implements the Amoeba torsion-torsion interaction |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) AmoebaVdwForce | This class implements a buffered 14-7 potential used to model van der Waals forces |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) AmoebaWcaDispersionForce | This class implements a nonbonded interaction between pairs of particles typically used along with AmoebaGeneralizedKirkwoodForce as part of an implicit solvent model |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) AndersenThermostat | This class uses the Andersen method to maintain constant temperature |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) Integrator | An Integrator defines a method for simulating a System by integrating the equations of motion |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) BrownianIntegrator | This is an Integrator which simulates a System using Brownian dynamics |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) CMAPTorsionForce | This class implements an interaction between pairs of dihedral angles |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) CMMotionRemover | This class prevents the center of mass of a System from drifting |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) Context | A Context stores the complete state of a simulation |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) CustomAngleForce | This class implements interactions between sets of three particles that depend on the angle between them |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) CustomBondForce | This class implements bonded interactions between pairs of particles |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) CustomCompoundBondForce | This class supports a wide variety of bonded interactions |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) CustomExternalForce | This class implements an "external" force on particles |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) CustomGBForce | This class implements complex, multiple stage nonbonded interactions between particles |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) CustomHbondForce | This class supports a wide variety of energy functions used to represent hydrogen bonding |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) CustomIntegrator | This is an Integrator that can be used to implemented arbitrary, user defined integration algorithms |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) CustomNonbondedForce | This class implements nonbonded interactions between particles |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) CustomTorsionForce | This class implements interactions between sets of four particles that depend on the torsion angle between them |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) GBSAOBCForce | This class implements an implicit solvation force using the GBSA-OBC model |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) GBVIForce | This class implements an implicit solvation force using the GB/VI model |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) HarmonicAngleForce | This class implements an interaction between groups of three particles that varies harmonically with the angle between them |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) HarmonicBondForce | This class implements an interaction between pairs of particles that varies harmonically with the distance between them |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) LangevinIntegrator | This is an Integrator which simulates a System using Langevin dynamics |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) LocalEnergyMinimizer | Given a Context, this class searches for a new set of particle positions that represent a local minimum of the potential energy |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) MonteCarloBarostat | This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) 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 |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) OpenMMException | This class is used for all exceptions thrown by OpenMM |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) VirtualSite | A VirtualSite describes the rules for computing a particle's position based on other particles |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) OutOfPlaneSite | This is a VirtualSite that computes the particle location based on three other particles' locations |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) PeriodicTorsionForce | This class implements an interaction between groups of four particles that varies periodically with the torsion angle between them |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) Platform | A Platform defines an implementation of all the kernels needed to perform some calculation |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) 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 |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) RPMDIntegrator | This is an Integrator which simulates a System using ring polymer molecular dynamics (RPMD) |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) System | This class represents a molecular system |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) ThreeParticleAverageSite | This is a VirtualSite that computes the particle location as a weighted average of three other particle's locations |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) TwoParticleAverageSite | This is a VirtualSite that computes the particle location as a weighted average of two other particle's locations |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) VariableLangevinIntegrator | This is an error contolled, variable time step Integrator that simulates a System using Langevin dynamics |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) VariableVerletIntegrator | This is an error contolled, variable time step Integrator that simulates a System using the leap-frog Verlet algorithm |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) VerletIntegrator | This is an Integrator which simulates a System using the leap-frog Verlet algorithm |
![](ftv2blank.png) ![](ftv2blank.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) XmlSerializer | XmlSerializer is used for serializing objects as XML, and for reconstructing them again |
![](ftv2blank.png) ![](ftv2blank.png) ![\](ftv2mlastnode.png) vec3 | |
![](ftv2blank.png) ![](ftv2blank.png) ![](ftv2blank.png) ![\](ftv2lastnode.png) Vec3 | Vec3 is a 3-element tuple that supports many math operations |