From: Ana Celia Araujo Vila Verde (
Date: Tue Sep 05 2006 - 11:13:06 CDT

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