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Water diffusion in equilibrium

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 $\to$ Label $\to$ 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.

next up previous
Next: Simulation with induced pressure Up: Water diffusion and permeation Previous: Submit your simulation;;