VMD-L Mailing List

From: Bob Johnson (robertjo_at_physics.upenn.edu)
Date: Fri Jun 01 2007 - 09:59:47 CDT

Hello everyone,
Sorry for this lengthy post, but my problem is a little bit complicated. I'm
trying to use the Volmap tool in VMD 1.8.6 to visualize the average charge
density in my system. My system consists of a carbon nanotube aligned along the
z-axis surrounded by a 1nm water layer. Since the nanotube atoms are neutral,
the only charges present are due to the water. The water is obviously very
mobile so I wanted to compute the charge density for each frame and combine
them using the average.

My system is cylindrically symmetric about the z-axis, so I can visualize the
water charge density with the VolumeSlice drawing method with the axis along z.
The charge density I see when viewed this way does not agree with the charge
density that I compute from a separate script. The calculated charge density in
the radial direction can be seen here:
http://dept.physics.upenn.edu/~robertjo/files/temp/rho-script.jpg

>From this plot, one can see that the water hydrogens are, on average, the
closest atoms to the nanotube which gives rise to a positive peak centered 2.5
angstroms away from the nanotube wall. However, this is not reflected in the
charge density that I compute and visualize with the VMD tools. An image of
what I see in VMD can be seen here:
http://dept.physics.upenn.edu/~robertjo/files/temp/nt-water-volslice.jpg
In this image, negative=red and positive=blue. As you can see, the nanotube is
surrounded by a negative region which is opposite what I get with the
calculated density. I believe the calculated one is correct because it gives the
correct result for the potential drop across the air-water interface.

To try to understand what was going on here, I used the VMD tools to compute and
visualize the charge density (computed with a 0.1 angstrom resolution) for a
single water molecule. The result looks different depending on whether I use
the Isosurface
(http://dept.physics.upenn.edu/~robertjo/files/temp/water-iso.jpg) or
Volumeslice
(http://dept.physics.upenn.edu/~robertjo/files/temp/water-volslice.jpg)
representations. The odd thing about the volume slice representation is that
there appears to be no negative region in the charge density. In all these
examples, I made sure that the color scale was symmetric about 0. Are there
some limitations with the resolution of the Volumeslice drawing method that
could explain this situation?
Thanks,
Bob Johnson