[gmx-users] about box size (II)

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sat Sep 23 11:17:27 CEST 2006

> when i change  the size to 6.0 (my  system is 3,2,6)
> ,the upper monolayer turn around ,the bottom to the top ,top to  the  
> bottom ,is it the too big size in the x and y direction? should i to  
> enlarge my sysytem to (6,6,6) to suit the box size?
> thanks!

Did you try the -d option that I suggested? It sounds like you used  
the -box option. Simply use the -d option. Choosing the membrane group  
for centering may leave you with a representation that is more  

You should not need to do this next part, but if you want to you can  
check the min and max values for x,y, and z in your .gro file like this:
1. copy the following script into a file called maxmin.pl
2. chmod +x maxmin.pl
3. ./maxmin.pl structure.gro

minx=`sort -n -k 4 $1 | head -1 | awk '{print $4}'`
miny=`sort -n -k 5 $1 | head -1 | awk '{print $5}'`
minz=`sort -n -k 6 $1 | head -1 | awk '{print $6}'`
maxx=`sort -n -k 4 $1 | tail -1 | awk '{print $4}'`
maxy=`sort -n -k 5 $1 | tail -1 | awk '{print $5}'`
maxz=`sort -n -k 6 $1 | tail -1 | awk '{print $6}'`
echo "x[$minx to $maxx]  y[$miny to $maxy]  z[$minz to $maxz]"

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