Hi,
Did you use the same mdp files provided in the tutorial? I also assume the reported estimate (-6.4 kJ/mol) is the average of three repeats.
Although we didn’t see a gromacs version dependence of the free energy estimates earlier on tripeptide (please have a look at this discussion Challenges in Reproducing ddG Estimation Results for 1STN - #11 by mstieffe), you can also try using the same gromacs version as the tutorial (just to confirm).