In this section, you will observe water movement through an array of
nanotubes under two types of simulation conditions, namely, free
water diffusion in equilibrium and directional water flow under
a hydrostatic pressure difference.
All simulations in this section are performed under
periodic boundary conditions, with constant temperature (300 K)
and constant volume. To make the simulations faster and analysis simpler,
all atoms in the nanotubes are fixed, i.e., only water molecules can move.
For water diffusion, you will look at a 3 ns
equilibrium MD simulation that has been provided to you in the form of an
already computed NAMD trajectory. Using this trajectory,
you will look at water orientation in the nanotubes as well as water
diffusion through the nanotubes. Then you will perform another
type of simulation, where a hydrostatic pressure difference is
induced through the application of forces on some water molecules.
In this simulation you will be able to observe a directional water
flow through the nanotubes. You will run a short simulation
(40 ps) of this type yourself, but we have also provided a
longer trajectory (1 ns), which you can use for your analysis.
Finally, you will look at a 1 ns MD trajectory of modified
nanotubes (with charges assigned to a few atoms), and find out
whether the water in the nanotubes behaves differently.