Dear experts, 1- I am trying to get interaction energies between solute (3 chains A) and solvent 50 molecules B. In the index file I created two groups: one for all atoms of [A] and and [B] for all solvent molecules. and by setting A and B as energy groups in mdp file I am getting break down as A-A, A-B and B-B with g_energy.
I am a little confused as I dont know if I need to create different groups for my solute to get interaction energies A-A, A-B and B-B. I mean do I need to have [A1] for solute chain 1 ...[A3] for chain 3? and then sent A1, A2, A3 in mdp file and run g_energy? if I need to specify different chains, then to get say A-A should I average over all possible A1-A2, A1A3, A2-A3, A1-B, A2,B...? I am really confused .. 2- I know it is naive question but What does A1-A1 mean? How can one chain interact with itself? 3- Do I need to use mdrun - rerun option to get beakdown or just g_energy gives what I need? Thanks for your help Paniz
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