Dear Justin Thanks for your quick reply. I did before: Thus, I should obtain new tpr file from new mdp file with the desired energygrps: grompp -f new.mdp -c *.gro -p *.top -o new.tpr Then, I should use mdrun -s new.tpr -o new.trr -e new.edr -rerun old.trr Are my manner and commands true? Best wishes