Re: vmd-l: imposing period boundary conditions in a simulation with a crystal

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Sep 05 2006 - 12:00:19 CDT

hi ana,

for the following i assume you are simulating a orthogonal unitcell.

your image looks as if you include the 'boundary atoms' twice.
see below for an example of what i mean.
say you have only 1-d PBC and the unitcell would contain
only two atoms, then the periodic crystall would be something like:
X--X--Y--Y--Z--Z--
however, when looking at the single unitcell people prefer
visualize it as:
X--X--X
with the X sitting exactly on the boundary.

so i would assume, your input would make more sense to you,
if you elminate the atoms that look strange to you and reduce
the length of the unit cell by 1 half X--X distance.

cheers,
   axel.

On 9/5/06, Ana Celia Araujo Vila Verde <avilaverde_at_engr.psu.edu> wrote:
>
> Hello all,
>
>
> I'm simulating water on a gold surface, but I'm having problems imposing the PBC's. In my case I have a gold crystal film in the XY direction (the gold atoms are fixed). So, as far as I understand, the number in cellBasisVector1 should be the length of the crystal slab in the X direction, plus the distance between the last atom of the crystal slab and the first atom on the periodic image (please see Fig. 1 attached; cellBasisVector1 = A+B, right?). However, when I do that and I subsequently visualize the crystal film and its images in VMD, I get an overlap between atoms of the original gold film and atoms of the gold film image (please see Fig. 2 and 3).
>
> Since I'm running simulations of the water on the gold, I think that "seam" at the boundary between the real system and the PBC system may cause local changes in the water's behavior.
>
> Could someone point out what I am misunderstanding here?
>
>
> Thank you for your time,
>
> Ana
>
> _________________________________
> Ana CÚlia Ara˙jo 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
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