From: Jervis Chu (nxchu_at_foxmail.com)
Date: Thu Jan 06 2011 - 01:06:18 CST

Dear Kohlmeyer,

Thanks for your kind reply. All done well for water molecules, but nothing happened on the XYZ file I mentioned. This really puzzled me.

The parameters of the representation are:

Coloring method: Name
Material: Glossy
Drawing Method: Dynamic Bonds
Distance Cutoff: 1.6
Bond Radius: 2.0
Bond Resolution: 6
Apply Changes Automatically: ON

Regards,

Jervis Chu
2011-01-06

Re: vmd-l: How to show dynamic bonds?

On Tue, Jan 4, 2011 at 2:58 AM, Jervis Chu <nxchu_at_foxmail.com> wrote:
> Hi,
>
> I generated an XYZ file, like
>
> 3
> atoms
> 1 0.0 0.0 0.0
> 1 1.6 0.0 0.0
> 1 2.9 0.0 0.0
> 3
> atoms
> 1 0.0 0.0 0.0
> 1 1.7 0.0 0.0
> 1 3.0 0.0 0.0
> ...
> ...
>
> All atoms are carbon.
>
> I want to show dynamic bonds in VMD with cutoff distance 1.6. Can anyone
> tell me how to do this on XYZ files.
sorry for stating the obvious, but have you tried using
the "Dynamic Bonds" representation???
axel.
>
> Thanks in advance.
>
> Regards,
> ________________________________
> Jervis Chu

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.