[gmx-users] Energy between desired selected molecules

[Faezeh Pousaneh]

Thank you both, I am close to solve it. The remaining problem is when I
mdrun -rerun, it tells the number of atoms in old trajectory is not the
same as chosen index file.

>Number of atoms in trajectory (24000) does not match the run input file
(16)

can you help me?
Best regards


On Fri, Jul 1, 2016 at 2:19 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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