[gmx-users] Energy between desired selected molecules

[Faezeh Pousaneh]

Hi

Does someone know how to obtain energy between specific molecules in the
system?

What I did and seems not be correct is:
1- I obtained the molecules I wanted to look at:
g_select_mpi -f 600gro.gro -s production.tpr -on

2- Then I produced a .tpr file for the chosen selection,index.ndx,
tpbconv -s production.tpr -n index.ndx -o tpxout.tpr

3- Finally put the created .tpr file as an input for g_energy
g_energy -f ener.edr -s tpxout.tpr  (either, g_energy -s tpxout.tpr)

But that is not the solution, since it gives energy for whole system.
Best regards