Modifying the VdW parameters

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 quite surprising.

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 lines:

  !atom  ignored    epsilon      Rmin/2
  CA     0.000000  -0.070000     1.992400
  HT     0.000000  -0.046000     0.224500
  OT     0.000000  -0.152100     1.768200

These 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.

Figure 6: 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 $\rightarrow$ 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.