VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Tue Jul 06 2004 - 14:18:34 CDT

On Tue, 6 Jul 2004, John Stone wrote:

hi,

AFAICT vmd does currently handle only orthorhombic unitcells correctly.

you may want to have a look at XCrySDen <http://www.xcrysden.org/>
and PWgui <http://www-k3.ijs.si/kokalj/pwgui/pwgui.html>. both are
Tk/tcl scriptable (like VMD), but since both are GPLed, the code itself
is probably not compatible to be included into VMD. a suitable
short/mid term approach could be to have some interface code in
vmd, that calls some external molecule/crystal editor. this could
also be of interest for other users.

axel.

JS>
JS> Dr. Sikorski,
JS> VMD doesn't implement any space group operators at the present time.
JS> It only implements the most simple degree of support for periodic systems,
JS> primarily suited for MD simulations with periodic boundary conditions.
JS> As yet we don't have the necessary infrastructure for performing more
JS> sophisticated symmetry-based transformations or queries, though this
JS> could be added with some work. At present I don't know enough about
JS> these topics to implement such code myself, so it's unlikely that I'll
JS> get to working on it in the near future. If someone else with experience
JS> in this area would like to help us develop the necessary routines,
JS> that would greatly accelerate the likely pace of development of this type
JS> of feature.
JS>
JS> Thanks,
JS> John Stone
JS> vmd_at_ks.uiuc.edu
JS>
JS> On Tue, Jul 06, 2004 at 01:24:40PM -0100, Pawel Sikorski wrote:
JS> > periodic display and space group
JS> >
JS> > Hi,
JS> > Does anyone know if it is possible, to generate symmetry related atoms
JS> > within the unit cell starting from an asymmetric unit and using space
JS> > group symmetry operators. Being able to inspect the results and move
JS> > things around would save a lot of work. Would appreciate any info.
JS> > Many Thanks
JS> > Pawel
JS> >
JS> > --
JS> > Dr.Pawel Sikorski
JS> > Room B4-103
JS> > phone: +47 735 98393
JS> > fax: +47 735 97710
JS> > http://www.phys.ntnu.no/~sikorski
JS> > Physics Dept. NTNU
JS>
JS> 

-- 
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Dr. Axel Kohlmeyer                        e-mail: axel.kohlmeyer_at_rub.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/
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