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