From: Axel Kohlmeyer (
Date: Tue Mar 25 2008 - 13:38:06 CDT

On Tue, 25 Mar 2008, Minhaj wrote:

M> Hello,

hello minhaj,

M> I am a newbie with VMD. I am trying to follow all the tutorials that I find
M> for VMD. I think I have learnt the basic usage of VMD. I am yet to find a
M> tutorial that talks about dealing with periodic solid crystals in VMD. I

that is probably because VMD is not exactly the fist tool that comes
into mind when doing these kind of things.

M> would like to learn how to create a, for eg. 2*2*1 super cell from a unit
M> cell (First off, if it is possible with VMD?) Any help is appreciated.

are you talking about coordinates or just visualization?
both is in principle doable. in the first case you have
to create a selection for the unit cell and then use
the "move" subcommand to translate the cell according to
your desires (a small fortran/c/perl/awk/python program
would do the same and which is probably what most people
use for this).
in the second case you just have to click on the respective
fields in the periodic tab of the individual graphical
representation. note, that this only replicates the visualization
(and hence does not compute any bonds etc across the unit
cell boundaries... if you want to see those you have to
use a different software, e.g. xcrysden.


M> Minhaj.
M> LouisianaTech University.

Axel Kohlmeyer
   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
If you make something idiot-proof, the universe creates a better idiot.