Trajectory

Molecular dynamics trajectory loading, playback, and analysis.

Shortcut

/traj <command> [args]

Commands

/trajectory load

Load a trajectory with topology.

/traj load topology.pdb trajectory.xtc

/trajectory loadall

Load all trajectories from a directory.

/traj loadall /path/to/md_runs/

/trajectory play

Start trajectory playback.

/traj play

/trajectory stop

Pause playback.

/traj stop

/trajectory info

Show trajectory information (frame count, time range).

/traj info

/trajectory frame

Jump to a specific frame.

/traj frame 50
/traj frame 0         # First frame

/trajectory speed

Set playback speed.

/traj speed 30        # 30 frames per second

/trajectory rmsd

Calculate RMSD over trajectory.

/traj rmsd backbone
/traj rmsd protein

/trajectory align

Align all frames to the first frame.

/traj align backbone

/trajectory record

Start/stop recording frames.

/traj record start
/traj record stop

/trajectory controllers

Show/hide playback controller panel.

/traj controllers