[gmx-users] index file for interaction energies
Justin A. Lemkul
jalemkul at vt.edu
Tue Feb 22 21:13:14 CET 2011
> 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?
If you want a breakdown of per-chain energetics, then yes, specify each chain as
a group. The programs will only do what you tell them, nothing more, nothing less.
> 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 ..
Theoretically, the short-range terms should sum, not average.
> 2- I know it is naive question but What does A1-A1 mean? How can one
> chain interact with itself?
Without knowing what the chain is, no one can answer this. Generally, any atoms
that are within the short-range cutoff and further away than nrexcl bonds
contribute to short-range interactions. Long-range interactions (i.e., PME
terms) happen too, but you can't decompose that term with energygrps.
> 3- Do I need to use mdrun - rerun option to get beakdown or just
> g_energy gives what I need?
You need to -rerun. g_energy does not take an index file, and it only analyzes
existing groups, it cannot derive new ones.
> Thanks for your help
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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