# Application Layer¶

 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