[gmx-users] Energy between desired selected molecules

[Faezeh Pousaneh]

Thank you Mark, I see. But what is the solution then? The way you proposed

''You can make a new .tpr file with those
energy groups and use mdrun -rerun on the old trajectory, however.''

 is not my answer, since I do not want the energy for a ''group'' of
molecules, rather for specified combination of few molecules I define from
g_select.


Best regards


On Fri, Jul 1, 2016 at 11:20 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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