Center the protein in the center of the dodechaodron box

User discussions
1

GROMACS version:2022.4
GROMACS modification: No

Dear users,

I am trying to center the protein in the center of the dodecahedron box before solvating but GROMACS doesn’t do it. Is it a bug?
But it works properly for the cubic box. I mean it centers the protein in the center of the cubic box.

Here is my command:
gmx editconf -f protein.gro -o newbox.gro -bt dodecahedron -d 1.2 -c

Thanks,

2

You have to re-wrap with gmx trjconv -pbc mol -ur compact after having generated a .tpr file to see the protein in the center of this kind of box.