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
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 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. 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.