Application Layer

Loaders and Setup

AmberInpcrdFile(file[, loadVelocities, …])

AmberInpcrdFile parses an AMBER inpcrd file and loads the data stored in it.

AmberPrmtopFile(file[, periodicBoxVectors, …])

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.

XTCFile(fileName, topology, dt[, firstStep, …])

XTCFile provides methods for creating XTC files.

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.

XTCReporter(file, reportInterval[, append, …])

XTCReporter outputs a series of frames from a Simulation to a XTC 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