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, resname, etc.
CharmmParameterSet(*args, **kwargs)	Stores a parameter set defined by CHARMM files.
CharmmPsfFile(psf_name[, …])	A chemical structure instantiated from CHARMM files.
CharmmRstFile(fname)	Reads and parses data, velocities and coordinates from a CHARMM restart file (.rst) of file name ‘fname’ into class attributes
DCDFile(file, topology, dt[, firstStep, …])	DCDFile provides methods for creating DCD files.
DesmondDMSFile(file[, verbose])	DesmondDMSFile parses a Desmond DMS (desmond molecular system) and constructs a topology and (optionally) an OpenMM System from it
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

BiasVariable(force, minValue, maxValue, …)	A collective variable that can be used to bias a simulation with metadynamics.
CharmmPSFWarning	For non-fatal PSF parsing issues
Element(number, name, symbol, mass)	An Element represents a chemical element.
Metadynamics(system, variables, temperature, …)	Performs metadynamics.
SimulatedTempering(simulation[, …])	SimulatedTempering implements the simulated tempering algorithm for accelerated sampling.

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