You need to do a special kind of simulation to estimate the free energy of your protein, in gromacs this is a basic example of how to free energy simulations:

http://www.mdtutorials.com/gmx/free_energy/index.html

Can you share the publication that this is from they are bound to have explained how they sample the free energy landscape of the protein.

Full disclaimer, my answer is probably very much incomplete as I haven't done much with free energy computations so far. Otherwise I would have given more specific advice.