Each molecule displayed by VMD can contain multiple sets of atomic coordinates, which may be played back to animate the molecule and show its motion. The source of the coordinates can be, for example, from a molecular dynamics simulation, or simply multiple versions of the same molecular structure. The Animate form is one way to control the playback of these trajectories.
The Animate form handles the trajectory playback of the active molecules. The second line of controls contains five buttons which act like the buttons on a tape player or VCR. The center button (with the square) stops the animation. The button to the right of the stop button advances the animation one step forward in the trajectory, and the next button to the right continually steps the animation forward. Similarly, the buttons to the left of the stop button steps the animation backwards either once or continuously. (Just remember that the button that looks like fast-forward is really the play button, and that the one that looks like the play button is really the single step forward button.)
The molecular status shown in this form reflects the state of the top molecule. Commands entered via this form, however, affect all active, not just the top molecule. This makes it possible to position several different molecules at the same frame, and to start them in motion at the same time with one command. But, since it is not immediately obvious from the information shown in this form what molecules will be affected, some care must be taken to make sure you have the proper molecules active that you wish to animate.
The rate of playback can be controlled in two ways. The Frame Skip controls change the step size. By default, the frame skip is 1, so each step of the playback increases (or decreases) the animation frame number by one. If the frame skip is 5 then the animation proceeds five times faster because only 1/5 of the frames are shown.
The Speed slider at the bottom of the form also affects the playback speed. Internally, this controls how many screen updates are needed between each step. By default, the slider is at the far right indicating that one step is performed for each screen redraw. Moving the slider to the left increases the minimum time required between updates.
The Start and End buttons are used to simplify the comparison between the initial and final structures - Start resets the current animation to the first frame, and End jumps to the last frame. If you need to jump to a specific frame, enter the frame number in the Jump To text area and press enter. One thing to bear in mind is that the frame number starts at 0, so to jump to the 5th frame, you must actually enter 4 here.
All of the controls affect the active molecules, but two parts of the animate menu use information from the top molecule. There is a display just below the End button which shows something like 0/1 or 23/59. The first number specifies the current frame number, starting at 0, and the second gives the total number of frames.
When the animation is playing forward and reaches the end of the data available for the top molecule, one of three possible actions takes place, as specified in the Style chooser. The default is `Loop', which will reset the active molecules to the first frame and continue playing forward. `Once' will stop the animation when it reaches the last frame, and `Rock' reverses the direction of animation. The actions are symmetrical when the animation is playing in reverse.