From: Axel Kohlmeyer (
Date: Tue Feb 07 2012 - 19:49:17 CST

On Tue, Feb 7, 2012 at 7:41 PM, niladri patra <> wrote:
> Hi ,
> I want to visualize the charge(or any other value) on each carbon atom of
> the given graphene-type structure (not by the colouring method).
> Lets say, on each carbon atom  there will be a pillar/column (along
> Z-direction) to represent the charge of that carbon and the height of the
> pillar will be according to magnitude of the charge.
> How can I do this type of visualization by vmd? Is there any script or
> plugin?

i see two possible strategies:

- you use the cylinder primitive (check out the graphics command)
  to draw cylinders "into the scene", that can be scripted, but most
  likely, you'll have to do that yourself.

- you can overlay a gnuplot graph on top of a VMD snapshot
  using gimp or photoshop or something similar. that may be
  easier to do, but more difficult to automate.


> Here is the input file. The last column contains the charge of
> corresponding carbon atom.
> ** By gnuplot I am able to make these pillar/column but I do not know how to
> make bonds between the carbon atoms.
> Thank You,
> Niladri Patra

Dr. Axel Kohlmeyer
College of Science and Technology
Temple University, Philadelphia PA, USA.