From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Mar 27 2007 - 15:48:22 CDT

On 3/27/07, Zheng Hu <zhuprivate_at_yahoo.com> 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.

you can just have two representations, VDW and DynamicBonds with
the appropriate radii to get a ball-and-stick with dynamics bonding.

> 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. )

what file format are you using? what program to generate the trajectory?
this looks like an angstrom/nanometer mixup.

axel.

>
> Thanks,
> Zheng
>
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-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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If you make something idiot-proof, the universe creates a better idiot.