[gmx-users] Energy between desired selected molecules

[Mark Abraham]

Hi,

Yes as Justin says, a group is a few molecules that you selected :-)

Mark

On Fri, 1 Jul 2016 14:00 Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/1/16 7:55 AM, Faezeh Pousaneh wrote:
> > 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.
> >
>
> The only function available is to define energygrps in the .mdp file,
> supply an
> index file with those groups (e.g. from g_select) and do as Mark says and
> re-calculate those interaction energies with mdrun -rerun on the existing
> trajectory.  The short-range nonbonded interaction energies between those
> groups
> will be written to their own terms in a new .edr file.
>
> -Justin
>
> >
> > 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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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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