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Next: ``Decorating" the nanotubes Up: Water diffusion and permeation Previous: Simulation with induced pressure

Water properties in modified nanotubes

So far, you have been looking at uncharged nanotubes. Now you will look at the effect of modifications of the nanotubes.

Here is your new system: a positive charge (+1e) is assigned to the center of the nanotubes, and two negative charges (-0.5e each) are assigned to the edges of the nanotubes. Other parts of the new system are exactly identical to your previous system. You will see later how you can do such a modification by changing the psf file.

We ran a 1 ns simulation on this new system, with induced pressure difference as described earlier. The simulation conditions were exactly the same as the previous simulation of the unmodified nanotubes. The trajectory is provided to you in the form of the file sim_mod.dcd available in the nanotubes working directory.

1. In VMD, create a new molecule with the files cnt_mod.psf and sim_mod.dcd.

2. Visualize the charges of the modified nanotubes: highlight the charges, by adding a CPK representation of atom selection carbon and charge!=0 in VMD, and choose Charge in the Coloring Method.

3. Observe water orientation in the modified nanotubes. Does the water orientation in the nanotubes now look very different than what you observed before? You should see a ``bipolar'' orientation here, in which the water molecules at the top and bottom of the channels are oriented along opposite directions. Play the trajectory. Is such a bipolar orientation well conserved during the simulation? You may want to pay particular attention to the water molecule in the center of each nanotube and the positively charged atoms there. Do they seem to be interacting strongly with each other?

4. Observe water permeation in modified nanotubes. Play the trajectory and look at the movement of single water files inside the nanotubes. Do they seem to move as fast as what you observed before in the unmodified nanotubes? Now count the net water flow in this 1 ns trajectory (you can do this by hand, or by using the script flow.tcl following earlier instructions). How does it compare to the water flow in the simulation of unmodified nanotubes (which were performed under the same conditions)? Now you may get an idea how much the permeation property of the nanotubes can be altered by introduction of charges. Think about the reason for such a difference.

next up previous
Next: ``Decorating" the nanotubes Up: Water diffusion and permeation Previous: Simulation with induced pressure;;