mdtraj.load_dcd(filename, top=None, stride=None, atom_indices=None, frame=None)

Load an DCD file from disk.

The .dcd format is a cross-platform compressed binary trajectory format produced by many software packages, including CHARMM, NAMD, and OpenMM. It stores atomic coordinates, box vectors, and time information.

Parameters
filenamestr

String filename of DCD file.

top{str, Trajectory, Topology}

DCD XTC format does not contain topology information. Pass in either the path to a pdb file, a trajectory, or a topology to supply this information.

strideint, default=None

atom_indicesarray_like, optional

If not none, then read only a subset of the atoms coordinates from the file. This may be slightly slower than the standard read because it requires an extra copy, but will save memory.

frameint, optional

Use this option to load only a single frame from a trajectory on disk. If frame is None, the default, the entire trajectory will be loaded. If supplied, stride will be ignored.

Returns
trajectorymd.Trajectory

The resulting trajectory, as an md.Trajectory object.

mdtraj.DCDTrajectoryFile

Low level interface to DCD files

Examples

>>> import mdtraj as md

>>> traj2 = md.load_dcd('output.dcd', stride=2, top='topology.pdb')