GROMACS version:2022.3
GROMACS modification: Yes/No
Here post your question :
I have prepared a system of protein osmolyte and water after NPT Equilibriation I analyse the gro file in vmd still the osmolytes are visible outside the box but as I increasing the d in gmx edit conf command the size increase the residue also but I have to make a system not sooo big so that my protein osmolyte all come inside it .What should I do so that if I increase d, box will become bigger and it will take a lot of time for simulation also as my protein consist of 140 residue it itself is big what should I do .
When you set up the system (before any MD run), the box ideally should be large enough to contain all the elements of your system and have enough space at the edges to avoid self-interactions with mirror images. In a protein/water system this is usually done by setting the -d flag in editconf to a number that is at least your electrostatics cut-off length (1.5nm usually works well to stay a bit conservative). This is supposing that the protein doesn’t have any major conformational change (e.g. partial unfolding) which would change sensibly the radial volume occupied by it.
I think what you are having is simply a problem of periodic boundary conditions which you can easily fix with trjconv.