VMD-L Mailing List

From: Ana Celia Araujo Vila Verde (avilaverde_at_engr.psu.edu)
Date: Fri Jun 23 2006 - 10:22:49 CDT

Hi all,
 
I am experiencing a problem with the "measure" command. I am using it to determine the minimum and maximum values of the coordinates in my simulation box and also its geometric center. In my case, I am simulating a droplet of water on gold.
 
If I calculate the minmax and the center for the water, I get perfectly reasonable values.
If I calculate the minmax and the center for the gold, I also get reasonable values
However, when I calculate the center for the entire system, I get a Z coordinate which is entirely unreasonable: 8.27, instead of the expected 25.6 !!!! Can someone help me understand what is going on here?
 
Please see below the output that I got:
 
water minmax
{82.4457626343 82.3411026001 12.1560001373}
{119.096755981 119.577102661 49.2019996643}
 water center
100.929145813 100.934669495 30.4673595428
 
gold minmax
 {0.0 0.0 2.03900003433}
 {201.860992432 201.860992432 8.15600013733}
gold center 100.930107117 100.930007935 5.09764385223

all minmax
{0.0 0.0 2.03900003433}
{201.860992432 201.860992432 49.2019996643}
all center
100.928276062 100.93032074 8.27163791656
 
 
 
Thanks,
 
Ana
 
 

_________________________________
Ana Célia Araújo 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
_________________________________