How to add molecules to a specific location in periodic box using gromacs?

Question

In gromacs using the commands, command_1

gmx insert-molecules -f run03.pdb -ci CL.pdb -o out.pdb -nmol 119

will distribute CL ions in the system randomly, but how to specify a specific location to put the ions or molecules. For example if my periodic box is $\pu{5*5*10 nm^3}$ I want to put the ions to the location of $\pu{x < 5 nm, y < 5 nm }$ but $\pu{ z > 8 nm}$ (of course randomly but specific) in another words top part of the box I have also tried, command 2

gmx genion -s ions.tpr -o out.pdb -p system.top -pname NA -nname CL -neutral

But this command only replaces the SOL molecules (water) or some another residue in system.

Can someone help me, many thanks may be some other software can edit the pdb file but adding lot of ions one by one is quite annoying.

Answer 1

GROMACS should be able to do this using the -ip -dr options associated with the tool insert-molecules.

I have not used this myself, but the GROMACS insert-molecules documentation seems to indicate that these will do what you want. (now that you have tried them and they do work... well, now we know.)

As was also mentioned in the comments by @Vasista, the venerable Packmol can do this too.