Description of the system

In the following exercises, you will be investigating the permeation of water through nanotubes, as a model for transmembrane permeation of substrates through channels. Before starting the simulations and analyzing them, let's have a look at the system that you will be using for your exercises. For the simulations you will be using a set of four nanotubes arranged side by side that separates two layers of water. This is, in fact, your unit cell, and in actual simulations will be replicated in three dimensions using periodic boundary conditions (PBC).

1. Start VMD, and load a new molecule with the files nanotubes.psf and nanotubes.pdb, located in the nanotubes-tutorial working directory. You should see four nanotubes arranged in a membrane with water on both sides. This is your unit cell. The dimensions of the unit cell are 24.07 by 20.85 by 34.00 Å$^3$.

We now wish to see what the periodic system will look like (since the NAMD simulation will be using periodic boundary conditions).

2. In VMD, open the TkCon console (from the Extensions menu), and set the periodic cell dimensions by typing:

molinfo top set a 24.07
molinfo top set b 20.85
molinfo top set c 34.

a, b and c refer to the periodic cell dimensions in x, y and z, respectively. The above commands tell VMD the dimensions of the periodic cell that you are using.

3. Replace the current representation to only show the nanotubes. Open the Representations window and enter carbon for the text selection, and VdW for the Drawing Method. Then choose the Display $\rightarrow$ Reset View menu item in the Main window. You should now see a top view of the nanotubes.

4. Now click on the Periodic tab in the Representation window. Making sure that your ``carbon" representation is selected, click on the +X, -X, +Y and -Y checkboxes to display more unit cells. Your molecule should now resemble Fig. 1.

Figure 1: The simulated nanotube array.

5. Now rotate the system sideways, uncheck all the $\pm$X and $\pm$Y checkboxes, and check the $\pm$Z boxes instead.

6. Add a water representation and make it periodic in Z as well, just like you previously did for the carbon nanotubes. Your molecule should now resemble Fig. 2.

Figure 2: The layers of nanotubes and water in the simulation.