Another strength of VMD lies in its ability to playback trajectories resulting from molecular dynamics simulations. A sample trajectory, alanin.dcd is provided in the proteins directory included with VMD. To load it, open the molecule file browser as described previously. Next click on the Browse button and select the alanin.psf file in the file browser. Once selected, press the Load button to load the structure file. Next, select the alanin.dcd file and load it as well. This will read the DCD trajectory frames into the same molecule with the previously loaded alanin.psf file.
In the display window you should see a simulation of an alanin residue in vacuo. It isn't particularly informative, but you can easily see that the structure is quite unstable in an isolated environment. After the DCD file has loaded, animation will stop. To see it again or to fine- tune playback, use the animation controls found at the bottom of the main VMD window. Press the button that looks like > to play the animation. Use the Speed slider at the bottom of the window to change the speed of playback. By rotating the molecule around, etc. you should get an idea about how the system destabilizes over the course of the simulation. The animation controls are generally similar to what you'd find on a DVD or CD player.