From: Axel Kohlmeyer (
Date: Fri Feb 25 2011 - 10:33:27 CST

On Fri, Feb 25, 2011 at 10:48 AM, Qiang Fu <> wrote:
> Dear VMD Users,
> I want to draw a figure to show a molecule adsorbed on a metal surface.
> However, there is no bond connection between metal atoms even  I used the
> CPK mode for display, which makes the current version of the figure
> unacceptable.

have you tried using a VDW representation (with reduced radius)
in combination with a DynamicBonds representation?


> From the discussions on the VMD Mailing list, I know that with the command
> "topo addbonds <ID1> <ID2>, one can add a bond between the two atoms <ID1>
> and <ID2>. However, there are as many as 64 atoms in our surface system,
> which makes it too complicated to achieve in the same way. I know the Tk
> Console script might be used to do so, but I have very very little knowledge
> about it.
> Could you please give me some help? I am very grateful if you could tell me
> some convenient way to add bonds among so many atoms within the metal
> surface. Thank you very much!
> Best Regards!
> Sincerely,
> Qiang Fu
> --
> Dr. Qiang Fu
> Major in computational chemistry
> E-mail:
> Profile URL:

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.