Jayanth Jeevanandam In GROMACS, we model pHs by setting the protonation states of titratable residues before running the simulation. This is done by setting the charge states in the *.itp file for your protein.

If you'd like to determine the protonation state for each amino acid in your protein, you can use a web server like PROPKA. There, you'll be able to set your desired pH (e.g. pH 8) and it will calculate the most likely protonation state of each amino acid.

link: http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/

If you're interested in modeling residues that get protonated or deprotonated during the simulation, you would have to use constant pH molecular dynamics (CpHMD) which is not currently available in GROMACS. You could try CHARMM or NAMD.

thanks for your valuable comment sir JD Tamucci