Application Layer

Loaders and Setup

AmberInpcrdFile(file[, loadVelocities, ...]) AmberInpcrdFile parses an AMBER inpcrd file and loads the data stored in it.
AmberPrmtopFile(file) AmberPrmtopFile parses an AMBER prmtop file and constructs a Topology and (optionally) an OpenMM System from it.
CharmmCrdFile(fname) Reads and parses a CHARMM coordinate file (.crd) into its components, namely the coordinates, CHARMM atom types, resid, resname, etc.
CharmmParameterSet(*args, **kwargs) Stores a parameter set defined by CHARMM files.
CharmmPsfFile(*args, **kwargs) A chemical structure instantiated from CHARMM files.
CharmmRstFile(fname) Reads and parses data, velocities and coordinates from a CHARMM restart
DCDFile(file, topology, dt[, firstStep, ...]) DCDFile provides methods for creating DCD files.
DesmondDMSFile(file) DesmondDMSFile parses a Desmond DMS (desmond molecular system) and
GromacsGroFile(file) GromacsGroFile parses a Gromacs .gro file and constructs a set of atom positions from it.
GromacsTopFile(file[, periodicBoxVectors, ...]) GromacsTopFile parses a Gromacs top file and constructs a Topology and (optionally) an OpenMM System from it.
PDBFile(file[, extraParticleIdentifier]) PDBFile parses a Protein Data Bank (PDB) file and constructs a Topology and a set of atom positions from it.
PDBxFile(file) PDBxFile parses a PDBx/mmCIF file and constructs a Topology and a set of atom positions from it.

Representation and Manipulation

Topology() Topology stores the topological information about a system.
Chain(index, topology, id) A Chain object represents a chain within a Topology.
Residue(name, index, chain, id, insertionCode) A Residue object represents a residue within a Topology.
Atom(name, element, index, residue, id) An Atom object represents an atom within a Topology.
Modeller(topology, positions) Modeller provides tools for editing molecular models, such as adding water or missing hydrogens.

Simulation

ForceField(*files) A ForceField constructs OpenMM System objects based on a Topology.
Simulation(topology, system, integrator[, ...]) Simulation provides a simplified API for running simulations with OpenMM and reporting results.

Reporting Output

CheckpointReporter(file, reportInterval) CheckpointReporter saves periodic checkpoints of a simulation.
DCDReporter(file, reportInterval[, append, ...]) DCDReporter outputs a series of frames from a Simulation to a DCD file.
PDBReporter(file, reportInterval[, ...]) PDBReporter outputs a series of frames from a Simulation to a PDB file.
PDBxReporter(file, reportInterval[, ...]) PDBxReporter outputs a series of frames from a Simulation to a PDBx/mmCIF file.
StateDataReporter(file, reportInterval[, ...]) StateDataReporter outputs information about a simulation, such as energy and temperature, to a file.

Extras

CharmmPSFWarning For non-fatal PSF parsing issues
Element(number, name, symbol, mass) An Element represents a chemical element.

Units

BaseDimension A physical dimension such as length, mass, or temperature.
BaseUnit Physical unit expressed in exactly one BaseDimension.
Quantity Physical quantity, such as 1.3 meters per second.
ScaledUnit ScaledUnit is like a BaseUnit, but it is based on another Unit.
SiPrefix Unit prefix that can be multiplied by a unit to yield a new unit.
Unit Physical unit such as meter or ampere.
UnitSystem A complete system of units defining the base unit in each dimension