VMD-L Mailing List

From: Morgan, Brittany (Brittany.Morgan_at_umassmed.edu)
Date: Wed Sep 23 2015 - 08:36:21 CDT

You could try redefining the size of the periodic cell to be a little bit bigger using "pbc set {X Y Z} -all".

http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/

________________________________
From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of Francesca Lønstad Bleken [FrancescaL.Bleken_at_sintef.no]
Sent: Wednesday, September 23, 2015 5:34 AM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: visualising unit cell "plus a little more"

Hi,

I would like to visualize the unit cell "plus a little more" in each direction in order to see all the atoms at the cell edges. I have found that you can extend the unit cell by multiple images in the graphical representations box under periodic, but is there a way to do this in non-integers? I imagine it should be possible in the console, but have not found it.

What I want is to show all atoms within -0.1 and 1.1 of the unit cell in all directions.

I think I can do this by making a 3x3x3 periodic structure and manually choose which atoms to be shown and not, but it would be great if there was a less cumbersome method to do this.

Best regards,
Francesca

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Francesca L. Bleken
Research Scientist, Ph.D.
Department for Nano and Hybrid Materials

SINTEF Materials and Chemistry

Mobile: +47 95 20 79 71
www.sintef.no<http://www.sintef.no/>
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