[gmx-users] g_lie useage

[Saman Shahriyari]

dear gmx users
i am trying to use g_lie tool regarding the fact i am a
 newbie to this. so i searched through the web for an appropriate 
protocol. although there are lots of staffs discussing the theory, but i
 couldn't find any thing describing the steps techniqally and with some 
details.
generally speaking, this is what seemed to me as the steps 
that i need to go through (it would be the kind of you to help me know 
if they are correct and what is missing):
1-runnig two md simulations for free and bond ligand (using PME)
2-
 doing the mdrun with -rerun flag by using the new .mdp (as is prepared 
in gmx forum: 
http://gromacs.5086.x6.nabble.com/Doubts-over-g-lie-usage-td5000130.html)
 and the old .tpr file.
3- using g-energy to extract Elj and Eqq from ligand simulation in water (using the outputs of step 2 ) 
4- using the g-lie command by introducing Elj and Eqq  to it, in order  to have the final free energies of binding.
i do appreciate your kind help
saman