From: Ana Celia Araujo Vila Verde (avilaverde_at_engr.psu.edu)
Date: Wed Sep 06 2006 - 08:31:59 CDT
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
However, when I do this it seems that I get something like:
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.
Ana CÚlia Ara˙jo Vila Verde
Penn State University
Department of Chemical Engineering
University Park, PA 16802
Phone: +(1) (814) 863-2879
Fax: +(1) (814) 865-7846
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
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:
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.
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 CÚlia Ara˙jo Vila Verde
> Penn State University
> Department of Chemical Engineering
> Fenske Laboratory
> University Park, PA 16802
> Phone: +(1) (814) 863-2879
> Fax: +(1) (814) 865-7846
-- ======================================================================= 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.
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