GROMACS version: 5.1.2
My question: Hello, I’d like to insert molecules into a box of size 4.5 4.5 6, but only on the top starting from z=5 (So between z=5 and z=6). How do we impose this constraint?
I would use gmx insert-molecules to make a 4.5x4.5x1.0 box of the molecule, then use gmx editconf -trans 0 0 5 -box 4.5 4.5 6 to put it on top. Then proceed as necessary.
You might need/want to separate the editconf command, and possibly to edit the box vector yourself in the gro file (last line in the file is the box vectors, you can use a text editor but be careful to not move the decimal points), if that does not work with these commands as-is.