Packmol to pack protein-water in simulation box

GROMACS version: 2022.4
GROMACS modification: Yes/No
Here post your question : I want to run a simulation of protein-water system. I want to pack the system using packmol. But I have a confusion as to how to choose box dimensions and how to decide how many water molecules I need to add, also if I want to add ions to the system using Packmol, then what about adding the ions.mdp file step used in GROMACS ? And after having the output file from packmol, from which step should I proceed in GROMACS (as ions.mdp file has not been added and also forcefield has not been applied)? As I am new to using Packmol, these questions may seem naive, but I hope if anyone can kindly help me with this.
Thank you

May I ask why it has to be specifically with packmol since GROMACS tool can easily solvate and put the correct amount of ions in the system?

The box dimensions are largely decided by the system you want to study, in general you should aim for the smallest box (to reduce the computational load) that is compatible with the cutoffs of the system, i.e., you want to avoid PBC artifacts.

If you have a simple protein-water system then also web-servers like CHARMM-GUI can help you build the starting box and can also provide “non-conventional” shapes to reduce the amount of atoms of the system.

@obZehn Actually with protein-water system I also have a protein-organic solvent and protein-interface systems. So someone suggested me that it’s easier to prepare the system using Packmol. But while doing it, I got confused about how to set the box dimensions and no.of solvent molecules.