Animation
One of VMD's unique features is its ability to play back
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.