mdtraj.load_xtc

mdtraj.load_xtc()

Load an Gromacs XTC file from disk.

Since the Gromacs XTC format doesn’t contain information to specify the topology, you need to supply the topology yourself.

Parameters:

filename : str

Filename (string) of xtc trajectory.

top : {str, Trajectory, Topology}

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

stride : int, default=None

Only read every stride-th frame

atom_indices : array_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.

frame : int, 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:

trajectory : md.Trajectory

The resulting trajectory, as an md.Trajectory object.

See also

mdtraj.XTCTrajectoryFile
Low level interface to XTC files

Examples

>>> import mdtraj as md
>>> traj = md.load_xtc('output.xtc', top='topology.pdb')
>>> print traj
<mdtraj.Trajectory with 500 frames, 423 atoms at 0x110740a90>
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