Now you will come back to the simulation that you submitted
at the beginning. First, let's learn something about the
background and motivation for this type of simulation.
In experiments, a typical method to study water channels
is to set up different concentrations of (impermeable) solutes on
the two sides of the channel, thus giving rise to an osmotic
pressure difference, and to measure the net directional water flux.
Obviously, the relationship between the water flux and the osmotic
pressure difference cannot be studied by equilibrium simulations.
It is known that an osmotic pressure is
equivalent to a hydrostatic
pressure. Therefore, if one can generate a hydrostatic pressure
difference in MD simulations, one could mimic the experiments
mentioned above. This can be done by applying a
constant force along the direction on a layer of bulk water molecules.
The force will induce a pressure gradient in the bulk water layer,
which results in a pressure difference on the two sides of the
nanotubes due to the periodic boundary conditions (refer to
One appealing feature of this method is that the amount
of pressure difference can be easily calculated and tuned, thus the results
can be compared to experiments quantitatively.
In the submitted simulation, a constant
force of 0.4 Kcal/mol/Å along the direction was
applied to a 5.4 Å-thick water layer. In every time step of
the simulation, the
force will be applied to the O atoms of water molecules whose coordinates
(in the unit cell of the periodic system) satisfy
Å or Å. This
is a fairly large force, but it is needed to induce a very fast
water flux that can be observed in a very short simulation time
(practically you can only afford a 40 ps simulation for the purpose of
this tutorial). You may take a few moment to inspect the NAMD
configuration file sim_short.conf for this simulation.
1. Check whether the simulation has already finished.
If not, wait a few minutes for it to finish (after 40,000 steps).
2. In VMD, create a new molecule with the
files cnt.psf and sim_short.dcd (the DCD file
generated by your simulation).
3. Play the trajectory and observe the water flow. Since water
molecules in the nanotubes move concertedly, you can label any of
them in a nanotube, and its movement will indicate the movement of
the whole water chain. Did you observe the drift of the water
chains toward direction in the trajectory? What is the net
water flow through the nanotubes during this simulation?
NOTE: The net water flow is in general different
from the number of permeation events. For example, when each
water molecule moves one step in the single file, effectively a
water molecule is transferred, thus resulting in a net water flow
of one water molecule, although this move may not cause a
permeation event. In the equilibrium simulation you looked at
earlier, there was little net water flow, although you observed a
lot of permeation events. In contrast, here in the present (short)
trajectory, you might not see any
individual water molecule crossing all the way through the
nanotubes, but you can observe a directional water flow.
The trajectory of your simulation (40 ps) is too short for
good statistics. Therefore, here we provide to you another trajectory,
which was run at exactly the same conditions as the simulation you
ran, except that this one is longer (1 ns), which allows you to
observe more water flow.
4. In VMD, delete all the frames of the current molecule
(which should be cnt.psf), by going to
Frames Delete. Then load into the DCD file sim.dcd,
by first selecting the cnt.psf molecule and then calling the File Load Data Into Molecule... menu item.
5. Observe the water flow in the long trajectory. Since the
total water flow is fairly large, it will be too tedious to count
it by hand. Therefore, we have provided to you a script,
flow.tcl, to count the water flow. In VMD, make sure
that the 1 ns trajectory is the ``top'' molecule, and then type in
the TKCon window source flow.tcl. The script will report the
amount of net water flow and its direction.
NOTE: While the script is running, VMD will freeze
and will not respond to other commands. Depending on your machine,
this may take 10-20 seconds.
Exercise: Can you calculate the hydrostatic pressure
difference in this simulation? The
pressure difference is . Here you know that is
0.4 Kcal/mol/Å, the unit cell of the periodic system has
dimensions of 23 Å 19.9 Å 30.4 Å, and , the number
of water molecules in the 5.4 Å-thick layer (water molecules
on which you are applying force), can be roughly
estimated by the volume of the layer and the molar volume of
water (55.5 mol/l). What is your calculated pressure difference?
How does it compare to one atmosphere (10 Pa)? Now you
may realize how ``hard'' it is to induce a significant water flow
within 40 ps.
6. You may also look at water orientation in the nanotubes
as water is being conducted. Does the fast
flow alter the water orientation that you had observed in the