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.
We now wish to see what the periodic system will look like
(since the NAMD simulation will be using periodic boundary
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 Reset View
menu item in the Main window. You should now see a top view of
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
5. Now rotate the system sideways, uncheck all the X and Y checkboxes, and check the 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