VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 27 2007 - 15:39:26 CDT

Hi,
  For dynamic bonding with older versions of VMD:
You can create dynamic bonding CPK/Licorice representations using
the DynamicBonds representation combined with the VDW representation
and setting the sphere/cylinder radii appropriately.

Starting with VMD 1.8.5, it is possible to enable dynamic
bond recalculation for all of the ball-stick representations,
through the use of Tcl commands. This feature isn't exposed
in the graphical interface yet (we need to redesign some of
the GUI to accomodate this and many other recently added features),
but you can enable the dynamic recalculation by passing an extra
flag (1 to enable dynamic bond recalculation) to the
CPK/Lines/Licorice representation commands, e.g.:
  mol modstyle 0 0 CPK 1.000000 0.300000 8.000000 6.000000 1

The behavior you're seeing with your atoms moving 1-2 A per step is
almost certainly the result of loading a structure with undefined or
mismatched coordinate units into VMD.
This typically occurs with the more "free-form" file formats such
as XYZ variants exported by many programs without any specified
coordinate units.

Since you didn't say what program generated your trajectory data
nor what file format your trajectory is stored in, I can't be sure,
but if you've indeed got incorrect coordinate units,
you can easily correct this with a simple Tcl script to scale them
to Angstroms, which are the internal units assumed by VMD.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 27, 2007 at 12:21:02PM -0700, Zheng Hu wrote:
> Dear VMD users,
>
> I want to show the dynamic connectivity. Does any plugin or scipt I can use for this purpose? I know the DynamicBonds in VMD can do that, but I want to represent moleculs in "stick and ball" mode.
>
> I want to report a bug in VMD too. I animate my simulation results using VMD. From visualization, it looks like that the displacement of atoms per step is more than 1-2 angstrom, but actually it's less that 0.02 angstrom. So the animation looks strange. ( My system is crystal struture of more than 4000 atoms. )
> Thanks,
> Zheng
>
>
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078