fixed atoms appearing on the other side of simulation box

From: Ana Celia Araujo Vila Verde (avilaverde_at_engr.psu.edu)
Date: Tue Jan 16 2007 - 13:38:33 CST

Hi,
 
I'm simulating a system containing water and gold using periodic boundary conditions and wrap all. The initial simulation box looks like this (dots =fixed atoms; /=atoms free to move):
 
 
//////////////////////////////////////////////
//////////////////////////////////////////////
//////////////////////////////////////////////
//////////////////////////////////////////////
//////////////////////////////////////////////
//////////////////////////////////////////////
//////////////////////////////////////////////
 . . . . . . . . . . . . . . . . . . . . . .
  . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . .
 . . . . . . . . . . . . . . . . ... . . . .
 
However, when I looked at the dcd half way through the simulation, I found that the last row of fixed atoms is now on top of the free atoms:
 
 . . . . . . . . . . . . . . . . ... . . . .
//////////////////////////////////////////////
//////////////////////////////////////////////
//////////////////////////////////////////////
//////////////////////////////////////////////
//////////////////////////////////////////////
//////////////////////////////////////////////
//////////////////////////////////////////////
 . . . . . . . . . . . . . . . . . . . . . .
  . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . .
 
 
Can someone explain why this is happening and whether it is a sign of something wrong with my simulation? I'm thinking that this is a consequence of "wrapAll on" but I'm uneasy about it because I thought fixed atoms wouldn't really be affected by wrapAll.
 
 
Thanks in advance for your attention. All the best,
 
Ana
_________________________________
Ana CÚlia Ara˙jo Vila Verde
Penn State University
Department of Chemical Engineering
Fenske Laboratory
University Park, PA 16802
USA
 
 <http://www.gfct.fisica.uminho.pt/Members/acvv>
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
_________________________________

 

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:57 CST