Complex not centered after editconf + solvate (GROMACS)

User discussions
1

GROMACS version: 2023.3
GROMACS modification: Yes/No
Hi everyone,
I’m facing an issue when preparing my system in GROMACS. After running the following commands:

gmx editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 1.0
gmx solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro

the complex is not centered inside the simulation box when I visualize it in VMD.
Has anyone experienced this before?
Thank you very much for your time

2

Is there any particular reason why you need your complex centered inside the box? Gromacs will not move the molecule for you until you explicitly ask it to (you can use -translate with editconf, or -center with trjconv).