Editconf with octahedral box

User discussions
1

GROMACS version: 2021
GROMACS modification: No
Dear all,
I am trying to build an octahedral solvation box with the following commands:

gmx editconf -bt o -d 2.0 -f eme_compl_gromacs.pdb -o eme_compl_gromacs_box.pdb

gmx solvate -cp eme_compl_gromacs_box.pdb -cs spc216.gro -o eme_compl_gromacs_wat.pdb -p eme_compl_gromacs.top

but after generating the box, opening it in vmd, it appears a cubic one with the protein not even centered.
Am I missing something?

Thanks
Stefano

2

That’s normal - all GROMACS utilities will write coordinates in a triclinic representation, which you can re-wrap once you have a .tpr file with gmx trjconv -ur compact.

3

Ok, thanks a lot.
Stefano