VMD-L Mailing List

From: Ana Celia Araujo Vila Verde (avilaverde_at_engr.psu.edu)
Date: Wed Sep 06 2006 - 08:31:59 CDT

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.

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
_________________________________

-----Original Message-----
From: akohlmey_at_gmail.com [mailto:akohlmey_at_gmail.com] On Behalf Of Axel Kohlmeyer
Sent: Tuesday, September 05, 2006 1:00 PM
To: Ana Celia Araujo Vila Verde
Cc: vmd-l_at_ks.uiuc.edu; namd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: imposing period boundary conditions in a simulation with a crystal

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 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.