Visualization of MD trajectories

Loading a MD trajectory

Load topology adk.psf with trajectory adk_dims.dcd.

Note

You always load a topology file first and then you load the trajectory data for the system.

  • load the topology file: File ‣ New Molecule

    • Load files for: New Molecule
    • Filename adk.psf
    • Determine file type: Automatically

  • load the trajectory file: In the Molecule File Browser

    • Load files for: 0: adk.psf
    • Filename adk_dims.dcd
    • Determine file type: Automatically
    • Load all at once: x

    (If you closed the Molecule File Browser, re-open it with File ‣ New Molecule.)

Note

Instead of using File ‣ New Molecule you can also select (highlight) your molecule in the main window (left click) and then use the File ‣ Load Data Into Molecule menu item.

Visualize

  • see Visualizing protein structure and topology from the previous practical for generally useful VMD settings and more details on selections and representations
  • Graphics ‣ Representations: color domains and show as new cartoon
    • protein and resid 30 to 59: blue (NMP domain of AdK)
    • protein and resid 122 to 159: yellow (LID domain of AdK)
    • protein and not (resid 30 to 59 122 to 159) (or protein and resid 1 to 29 60 to 121 160 to 214): gray (CORE domain of AdK)

Play a trajectory

VMD can show a trajectory frame by frame. Trajectory play is controlled through the main window.

  • play with the ▶ the right triangle button
  • set Loop to Rock (makes trajectory move forward and backward)
  • use the slider to manually move through the trajectory (note how the frame number changes)
  • enter a new frame number in the frame number widget and press enter to jump to the frame