Here, you will learn how to modify the VdW radius of a certain
type of atom in a NAMD simulation. you will significantly reduce the
radius of the nanotube's carbon. This will make the pore wider.
Question: Try to predict what will happen if you make
the nanotube wider. As you will soon see, the answer to this will be
1. Make a copy of the par_nanotubes.inp parameter file
(let's call it par_mynanotubes.inp; it is very important that
it starts with par_ and ends in .inp!) and open it in a
text editor. Near the end of the file, you should see the following
!atom ignored epsilon Rmin/2 CA 0.000000 -0.070000 1.992400 HT 0.000000 -0.046000 0.224500 OT 0.000000 -0.152100 1.768200These lines specify the van der Waals parameters for each given atom type, which will be used by the NAMD simulation. Fig. 6 shows the meaning of the epsilon and Rmin/2 parameters in the van der Waals potential energy function.
2. Reduce the VdW radius parameter by a factor of 4 for all the CA atoms, by editing the line:
CA 0.000000 -0.070000 1.992400
so that it now says:
CA 0.000000 -0.070000 0.5
3. Save your changes to the parameter file.
4. To run an AutoIMD simulation with this new parameter file, you
need to open AutoIMD's Settings Simulation
Parameters... window. Completely erase the contents of the
CHARMM params line, click on Add... and then
select your modified par_mynanotubes.inp file. Your next
AutoIMD session will use these modified parameters.
5. Make sure that you are using an uncharged nanotube by
reloading the original imdnanotube.psf PSF file back into your
molecule again (to override your previous changes).
6. Finally, start AutoIMD (by clicking on AutoIMD's Submit button, etc.) and observe what happens to the water
file after 10-20 ps.
If you are surprised, do you think that you could have
predicted what just happened? In order to explain why the water
departed from the pore, it might be helpful if you used VMD to
display both the nanotube and the permeating waters by using the
VdW Draw Style. In order to display, the carbons'
approximate size, you can shrink their VdW Sphere Radii (in the VMD
Representation window) by a factor of 4 (i.e., Sphere Radius = 1.0/4 = 0.2-0.3). By inspection, what can you say
about the water-nanotube interaction with the big and the small
carbons. Remember that at the VdW radius (i.e. when the
``spheres" touch) the VdW interaction is maximally attractive.