VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 13 2004 - 13:42:52 CDT

Hi,
  As Axel mentioned, there isn't a way to draw bonds between periodic
images yet. His suggestion does provide a practical solution to this
problem until we add that capability. The most tricky aspect of adding
such a feature is that it'll have to be taught to interact well both with
auto-determined bonds (distance-based bond determination code) as well as
with structures loaded from PSF files or other formats that provide bond
information but don't necessarily do anything special for periodic systems.
For the time being, I'd recommend following Axel's suggestion and I'll see
if we can add this in a future rev of VMD.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Apr 13, 2004 at 06:27:30PM +0200, Axel Kohlmeyer wrote:
> LV> there's one more question arising... if you turn periodic images of the
> LV> unit cell on - is there any way how to force vmd to draw bonds between
> LV> the periodic images, i.e. in my case to connect the whole zeolite framework?
>
> vmd does not do that automatically (yet?). but how about adding replica
> of one layer of atoms_outside_ of the box so that you'll be able
> to set/get the bonds. if you set the box size correctly, the periodic
> images overlap perfectly with the additional atoms/bonds.
>
> axel.
>
> LV> regards,
>
> LV> --
> LV> Lubos
> LV> _@_"
>
>
>
> --
>
> =======================================================================
> Axel Kohlmeyer e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
> Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673
> Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045
> D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot. 

-- 
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