I'd like to put the peptide molecule on the surface of a membrane, instead of inside, to observe affinity and capacity of trespassing the bilayer barrier. How can I do that on GROMACS?
You can position any entity wherever you want within the unit cell with editconf. See, for example: http://www.mdtutorials.com/gmx/biphasic/03_tricks.html
I would suggest you to equilibrate your bilayer in water without the peptide before adding the peptide, then take away the water, put the peptide, then add water again. If you put the peptide in the system containing a non-equilibrated bilayer the peptide might get mixed with it, then your goal might not be obtained.