VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Oct 13 2006 - 11:15:36 CDT

On Thu, 12 Oct 2006, Rob wrote:

R>
R> Hi all,

rob,

R> I use VMD exclusively with the VASP interface, but
R> I think my question applies to general shortcomings
R> of VMD. I'm currently using VMD 1.8.5.

please keep in mind, that VMD was not designed for
these kind of problems and especially if you are
using non-orthogonal supercells, you may face problems,
if the plugin does not rotate everything according
to VMDs internal conventions for periodic systems.

people are working on making VMD more welcoming
for these kind of visualizations, but some of
it will need some fundamental changes to the VMD
code and that will take a while since all other
functionality (and performance) has to be preserved.
 
R> When I load simply the coordinates of a set of atoms
R> in a unit cell, I can see the periodic replications
R> by checking the Periodic checkboxes in the window
R> of the "Graphical Representations".
R>
R> However, when I load volumetric data (e.g. in VASP
R> this is the charge density), the periodic checkboxes
R> are there but they don't work at all. Is this a bug?

the checkboxes are _always_ there. did you load the
volumetric data set 'into' an existing 'molecule'?
that usually works well.
for periodic display VMD needs the information of the
box dimensions. you can also set this manually from
the script interface (using molinfo set). see the vmd
manual.

cheers,
   axel.

R> I really would like to extend this volumetric data
R> according to the periodic boundary conditions, so
R> that I can replicate both the atoms and the
R> corresponding volumetric data.
R>
R> Regards,
R> Rob.
R>
R>
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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
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.