Here, you will look closely at a long (3 ns) trajectory
of an MD simulation in equilibrium, which shows free water
diffusion through the nanotubes. The respective simulation
has been already computed and the results are provided to you in
the nanotubes working directory.
1. In VMD, delete the molecule that you loaded in the previous
section, and create a new molecule by loading the files
cnt.psf and eq.dcd. Loading the trajectory might take a minute or two.
2. Create different representations for nanotubes and water.
You can use atom selections carbon and water,
for nanotubes and water, respectively. Feel free to choose your
favorite Drawing Method and Coloring Method for these
representations.
3. Observe water orientation inside the nanotubes. Also look at
how the water molecules are aligned. You should find that water
molecules in the same nanotube are all aligned along the same
direction (i.e., either all with their O atoms up and H atoms down, or
all with H atoms up and O atoms down). Think about why they prefer
such a concerted alignment. Play the trajectory with the VMD animation
controls, and see whether the orientation remains stable during the
simulation. In particular, did you observe any flipping of their
orientation? (If yes, how many times?)
4. Observe single file water diffusion. To identify individual
water molecules, you can label a couple of them in a nanotube (choose
Mouse 
Label Atoms in VMD). Now play the
trajectory. How do water molecules move with respect to each other? Is
any water molecule ever found to pass another one in the nanotube?
Otherwise do they always move in concert? Also look at the direction
of the water movement in nanotubes. Does it move back and forth, just
like one-dimensional Brownian motion?
5. Observe permeation events. A permeation event is defined
as a water molecule entering from one end of a nanotube and
leaving the other end, therefore traversing the entire
length of the nanotube. Can you find some of the permeation events
in the trajectory? Obviously, it is a tedious job to find all of
them in a long trajectory. So we provide a script,
permeation.tcl, to
help you. To use the script in VMD, you should first make sure
that the trajectory to be analyzed is the ``top'' molecule. Then
open the TkCon window in VMD and after making sure you are in the
files directory, type into the window:
source permeation.tcl
NOTE: While the script is running, VMD may appear to freeze
and not respond to other commands. Depending on your machine,
this may take 10-30 seconds.
The script will list the resid number of all the water molecules permeating
through the nanotubes, the frame at which the permeation
event completes, and its direction into the TKCon window.
You can pick a few water molecules from the
list, and check whether they have indeed completed the permeation
event as reported by the script. In the last two lines of the
output, the script also tells you the total number of permeation
events in each direction. Are the two numbers close to each
other, as would be expected?
Some additional details: You won't find any permeation events
in the very beginning (say, the first 200 ps) of the trajectory. This is
because for water molecules initially inside a nanotube, you don't know from
which end of the nanotube they had entered. Consequently, when they
leave the nanotubes, no permeation event can be counted. Therefore, for
quantitative study, the beginning portion of the trajectory
is usually excluded from statistics.
In your case, the numbers of permeation events
reported by the script permeation.tcl do not include those
in the first 500 frames (500 ps), thus are actually for permeation events
within the last 2.5 ns of the simulation.
6. After all of the above steps are done, delete the
molecule from VMD, since it takes up a significant amount of memory
in your machine.