while using the command :-
gmx grompp -f nvt.mdp -c proteinem.gro -r proteinem.gro -p protein.top -n index.ndx -o nvt.tpr -maxwarn 1
getting the error:-
2 atoms are not part of any of the T-Coupling groups
I have kept “tc-grps = Protein_SUB Water_and_ions” in nvt.mdp file
The error says the Protein_SUB and Water_and_ions groups do not contain all the atoms of the system. Those groups are defined in the index.ndx file. You may want to check the group are properly defined in the index file.
I also saw that you use the option -maxwarn. Maybe the warning may help you to understand which are the missing atoms.