[gmx-users] index file for interaction energies

[Nick]

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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