[gmx-users] Energy between desired selected molecules

[Mark Abraham]

Hi,

The .edr file contains only what was written during the simulation, and
that was for any energy groups defined before that run. You're trying to
ask it to make an arbitrary repartition, which it can't do unless it
recorded every component of the energy for every frame (which would take
forever and use lots of disk). You can make a new .tpr file with those
energy groups and use mdrun -rerun on the old trajectory, however.

Mark

On Fri, Jul 1, 2016 at 9:41 AM Faezeh Pousaneh <fpoosaneh at gmail.com> wrote:

> 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
> --
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