VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Sep 06 2006 - 09:23:39 CDT

On 9/6/06, Ana Celia Araujo Vila Verde <avilaverde_at_engr.psu.edu> wrote:
> Hi Axel,
>
> Thank you for your reply. However, my problem is still here. Following your own example of a 1-D PBC, this is what I did:
> Considering that my unit cell only has 2 atoms, but that I have 3 unit cells in my real gold film (a--a'--b--b'--c--c'), I put in cellBasisVectorX the sum of the distance between a and c' and the distance a--a'.
>
> By doing this I expect to see in VMD
>
> ...--(a--a'--b--b'--c--c')--(a--a'--b--b'--c--c')-- ...
>
> However, when I do this it seems that I get something like:
>
> ...--(a--a'--b--b'--c-(a-c')-a'--b--b'--c--c')-- ...
>
> That is, the first atom of the second cell comes before the last atom of the first cell.
>
> This happens even though I know the distance I put in cellBasisVectorX is correct (I checked a number of times).
>
> If anyone can provide a clue as to what I am doing wrong, I'd really appreciate it.

is your unit cell orthorhombic?

assuming your input is correct, the only way this effect
could happen with VMD is, if you have non-orthogonal
unit cell vectors. VMD expects a certain orientation of
the cell vectors to display images non-orthogonal unitcells
correctly (basically the PBC code was writting as if it
assumes only that kind of geometry). for the cube file
plugin (and .xsf and VASP, IIRC) the coordinates are
actually rotateted to accomodate that assumption.

it would be nice, if we could check out the files you have.
if you don't mind, please register at biocore
( http://www.ks.uiuc.edu/Research/biocore/ ) and join
the VMD (Public) project. you can then upload your files
to the BioFS and we can have a closer look. please
_don't_ post them to the mailing list(s). thanks.

cheers,
   axel.

>
> Thanks,
>
> Ana
> _________________________________
> Ana Célia Araújo Vila Verde
> Penn State University
> Department of Chemical Engineering
> Fenske Laboratory
> University Park, PA 16802
> USA
>
>
> Phone: +(1) (814) 863-2879
> Fax: +(1) (814) 865-7846
> avilaverde_at_engr.psu.edu
> http://www.che.psu.edu/Faculty/JMaranas/group/avv.html
> http://www.gfct.fisica.uminho.pt/Members/acvv
> _________________________________
>
> 

-- 
=======================================================================
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.