[gmx-users] editconf not centering, and it is cutting off my molecule

[Xu Dong Huang]

Dear advanced gromacs users,

I have created an arbitrary molecule .gro file containing coordinates of my martini-beads. basically, there are 50 beads sitting on each axis of (x,y, -x and -y) forming like a cross. (Each bead with distance 0.43). However, when I try to use editconf on my .gro file to generate a box (editconf -f star.gro -o star_box.gro -c -d 1.0 -bt cubic) , it gives me back a new .gro file with a bad molecule. In VMD viewing, I see that the negative axis part of my molecules are cut off. Closer inspection shows the following for a particular segment of the molecule coordinates: 

**original .gro coordinates: 
    1star     O1     170   0.000  -8.170   0.000 
    1star     O1     171   0.000  -8.600   0.000 
    2star     O2     172   0.000  -9.030   0.000 
    2star     O2     173   0.000  -9.460   0.000 
    2star     O2     174   0.000  -9.890   0.000 
    2star     O2     175   0.000 -10.320   0.000 
    2star     O2     176   0.000 -10.750   0.000 
    2star     O2     177   0.000 -11.180   0.000 
    2star     O2     178   0.000 -11.610   0.000 
    2star     O2     179   0.000 -12.040   0.000 
    2star     O2     180   0.000 -12.470   0.000 
    2star     O2     181   0.000 -12.900   0.000 
    2star     O2     182   0.000 -13.330   0.000 
    2star     O2     183   0.000 -13.760   0.000 
*new .gro coordinates: 

1star      O1      169  12.421   4.681  16.695 
    1star      O1      170  12.421   4.251  16.695 
    1star      O1      171  12.421   3.821  16.695 
    2star      O2      172  12.421   3.391  16.695 
    2star      O2      173  12.421   2.961  16.695 
    2star      O2      174  12.421   2.531  16.695 
    2star      O2      175  12.421  22.741  16.695 
    2star      O2      176  12.421  23.171  16.695 
    2star      O2      177  12.421  23.601  16.695 
    2star      O2      178  12.421  24.031  16.695 
    2star      O2      179  12.421  24.461  16.695 
    2star      O2      180  12.421  24.891  16.695 
    2star      O2      181  12.421  25.321  16.695 
    2star      O2      182  12.421  25.751  16.695 
    2star      O2      183  12.421  26.181  16.695 

Notice the jump on atom number 174 and 175, why is there a sudden coordinate jump? 
All i can see in VMD is my negative axis part of the molecule beads are cut off. 

Any input is appreciated. Thank you!

Xu Dong Huang
Chemical & Biochemical Engineering-Undergraduate Researcher
Rutgers School of Engineering 
xudongh at eden.rutgers.edu