# 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