One of VMD's unique features is its ability to playback trajectories from molecular dynamics simulations. We will explore this powerful feature with the help of a bR trajectory file provided by Barry Isralewitz of the University of Illinois. VMD has two main forms for controlling animations: the Animate form and the Edit form. The former offers VCR-like controls for playback, while the latter is used to append or delete frames to the animation. At this time you should have the PDB file of the bacteriorhodopsin loaded and on screen. We wish to append additional frames of an animation to this set of coordinates. Thus we will use the edit menu. Once you have activated this menu, be sure that the Action setting is "Read File," the Amount is "All", and the File Type is DCD. This file type is supported by many common molecular dynamics programs such as NAMD and X-PLOR. One DCD file usually contains many animation frames.
Go ahead and click the "Read" button on the edit form. In the FileSelector which appears, make sure the directory is /nfs/cairo/workshop and choose bR.dcd. Click Ready and you will begin reading in the simulation frames. As it loads, you will notice that the retinal is being pulled out from the center of the bacteriorhodopsin through a hole between two of the alpha helices. The objective of Isralewitz's study was to test whether or not this hole provides a possible route through which retinal can enter the bR protein. If pulling it out through this hole keeps the structure intact, then the reverse entry process may also be feasible. Try representing the retinal as "licorice" to make it easier to see this happening. (Use segname "RET" to select all atoms of the retinal.)
To control the playback of the trajectory, activate the animate form. You will see familiar looking forward, rewind, and stop buttons. Go ahead and play with these controls and the other options on the animate menu to see how they affect playback. Also notice that the total number of frames and the current frame counter are printed in the right hand corner of this menu.
The ability to visualize trajectories is a powerful tool in itself, but its benefits can be even more pronounced when combined with other VMD features. Let's look at an example. As the retinal leaves its binding pocket, it seems as though it gets hung up along several points of its exit path. It is likely that hydrogen bonds are forming and breaking in these locations. VMD can emulate this hydrogen bonding network using the HBonds drawing method. To see how this works, open the graphics menu and generate three different representations. (Remember, to generate multiple representations, use the "Create New" button at the bottom of the menu. To delete representations, use the corresponding delete button.) Click on the first representation (i.e. the top line in the blue browser window) and type segname RET in the atom selection box. For the other two representations we will take advantage of VMD's "within" command to select all atoms within five Angstroms of the retinal. These are the atoms likely to be involved in hydrogen bonding. Click on the second line of the blue browser window and type within 5 of segname RET in the text entry box. Choose Lines as the drawing method. Click on the third line of the blue browser window and again type within 5 of segname RET. This time, however, choose HBonds as the drawing method. At the bottom of the graphics menu you will see options which determine how hydrogen bonds are calculated and displayed. The Angle option has a rather conservative value. We suggest you bump it up to 25. Finally, scale the image in the display window so that the dashed hydrogen bonds are clearly visible to you. To see how this hydrogen bonding network changes over the course of the simulation, go back to the animate form and hit the play button.