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
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