[gmx-users] How to make all parts of a protein in the periodic box in when running "gmx editconf" command

[sunyeping]

Dear all, 

I run the"gmx editconf" command to make a periodic cubic box around my protein for adding water:

  gmx editconf -f protein.gro -o newbox.gro -c -d 1.0

Then I visualize the priodic box in VMD. I find that one end of my protein is out of the box (Please see the part in red circle in image at https://drive.google.com/file/d/1M6msh1UA0fOZ4GOuGJVlJHTOtHrzwh7u/view?usp=sharing). Even if I  increase the value of "-d" option to 1.5, this end of the protein is still out of the box. This will result in visualization problem of the MD trajectory. This part at one end of the molecule which is out of the box will jump to the other end of the molecule in VMD and pymol. Please see the part in the red circle in the image at (https://drive.google.com/file/d/1GAP4oS78nAB6p-ZhPmT9A-6ZZnohhkeq/view?usp=sharing). The is the image for em.gro the structure after energy minimization.  The trjconv command with -pbc cluster -center -ur cpmpact command cannot solve the problem. 

So could you tell me how to keep all part of the protein in the periodic box when running "gmx editconf" command? Thank you in advance.

Yeping