mdtraj.reporters.DCDReporter

class mdtraj.reporters.DCDReporter(file, reportInterval, atomSubset=None)

DCDReporter stores a molecular dynamics trajectory in the CHARMM / NAMD DCD Format

Parameters

filestr, or DCDTrajectoryFile

Either an open DCDTrajectoryFile object to write to, or a string specifying the filename of a new DCD file to save the trajectory to.

reportIntervalint

The interval (in time steps) at which to write frames.

atomSubsetarray_like, default=None

Only write a subset of the atoms, with these (zero based) indices to the file. If None, all of the atoms will be written to disk.

Examples

>>> simulation = Simulation(topology, system, integrator)
>>> dcd_reporter = DCDReporter('traj.dcd', 100)
>>> simulation.reporters.append(dcd_reporter)
>>> simulation.step(10000)

>>> traj = mdtraj.trajectory.load('traj.dcd')

Attributes

backend

Methods

close(self)	Close the underlying trajectory file
describeNextReport(self, simulation)	Get information about the next report this object will generate.
report(self, simulation, state)	Generate a report.

__init__(self, file, reportInterval, atomSubset=None)

Create an OpenMM reporter

Parameters

filestr, or HDF5Trajectory

Either an open HDF5Trajecory object to write to, or a string specifying the filename of a new HDF5 file

reportIntervalint

The interval (in time steps) at which to write frames.

coordinatesbool, default=True

Whether to write the coordinates to the file.

timebool, default=True

Whether to write the current time to the file.

cellbool, default=True

Whether to write the current unitcell dimensions to the file.

potentialEnergybool, default=True

Whether to write the potential energy to the file.

kineticEnergybool, default=True

Whether to write the kinetic energy to the file.

temperaturebool, default=True

Whether to write the instantaneous temperature to the file.

velocitiesbool, default=False

Whether to write the velocities of each atom to the file

atomSubsetarray_like, default=None

Only write a subset of the atoms, with these (zero based) indices to the file. If None, all of the atoms will be written.

Notes

If you use the atomSubset option to write only a subset of the atoms to disk, the kineticEnergy, potentialEnergy, and temperature fields will not change. They will still refer to the energy and temperature of the whole system, and are not “subsetted” to only include the energy of your subsystem.

Methods

__init__(self, file, reportInterval[, …])	Create an OpenMM reporter
close(self)	Close the underlying trajectory file
describeNextReport(self, simulation)	Get information about the next report this object will generate.
report(self, simulation, state)	Generate a report.

Attributes

backend

close(self)

Close the underlying trajectory file

describeNextReport(self, simulation)

Get information about the next report this object will generate.

Parameters

simulationsimtk.openmm.app.Simulation

The Simulation to generate a report for

Returns

report_descriptiontuple

A five element tuple. The first element is the number of steps until the next report. The remaining elements specify whether that report will require positions, velocities, forces, and energies respectively.

report(self, simulation, state)

Generate a report.

Parameters

simulationsimtk.openmm.app.Simulation

The Simulation to generate a report for

statesimtk.openmm.State

The current state of the simulation