[gmx-users] Energy decomposition

[Mark Abraham]

Hi,

Did you see my reply last week?

Mark

On Tue, Jul 31, 2018, 10:19 Vito GENNA <vito.genna at irbbarcelona.org> wrote:

> Dear all,
>
> I have followed the procedure you have suggested (vide infra).
> Now I have a trajectory only containing my selected atoms and its related
> .tpr file.
> However, after running g_energy and selecting "total energy" I get an
> energy value which is too high in my opinion (i.e. 3.98246e+06 kj/mol).
> I feel something is going wrong. Have you got any idea?
>
> Furthermore, if I would decompose this total energy in bond term, stretch
> term, angle term etc etc, which would be the best way to do it?
>
> Thanks in advance for your contributions.
>
> V
>
> On Wed, Jul 25, 2018 at 1:32 PM, Vito GENNA <vito.genna at irbbarcelona.org>
> wrote:
>
> > Dear all,
> >
> > I have followed the procedure you have suggested.
> > Now I have a trajectory only containing my selected atoms and its related
> > .tpr file.
> > However, after running g_energy and selecting "total energy" I get an
> > energy value which is too high in my opinion (i.e. 3.98246e+06 kj/mol).
> > I feel something is going wrong. Have you got any idea?
> >
> > Furthermore, if I would decompose this total energy in bond term, stretch
> > term, angle term etc etc, which would be the best way to do it?
> >
> > Thanks in advance for your contribute.
> >
> > V
> >
> > On Sun, Jul 8, 2018 at 8:06 PM, Vito GENNA <vito.genna at irbbarcelona.org>
> > wrote:
> >
> >> Dear GMXusers,
> >>
> >> I am writing you in the hope to find a solution to my problem.
> >>
> >> I'd love (and truly love) calculate the intramolecular energy (both
> >> bonded and non-bonded terms) of a DNA backbone for which I have a .xtc
> >> trajectory (and of course coords).
> >>
> >> What I did:
> >>
> >> 1) defined the index.ndx for each DNA strand and generated a ndx.file
> >> cotaining [strand-1] and [System - (strand-1)] (works fine)
> >>
> >> 2) Changed the energygrps in the mdp file to: [strand-1]  [System -
> >> (strand-1)] (works fine)
> >>
> >> 3) Generated a .tpr file selecting (from point 1) the .ndx of my
> interest
> >>
> >> 4) with mdrun with -rerun option (by using the .tpr of my interest
> >> generated at the previous stage) I get the .edr file [strand-1]
> >>
> >> 5) by using g_energy I only get Lennard-Jones and Coulomb terms (both
> >> short and long for [strand-1]:[strand-1]) while I would also include the
> >> bonded-terms.
> >>
> >> 6) The option ETOT, provided by g_energy, I guess does not return the E
> >> of the strand, rather of the overall system. Isn't it?
> >>
> >> Since I am comparing the same system in different conditions (then in
> >> different MD) I am looking for a strategy which would allow me to
> >> extrapolate all the energy terms for the backbone in a consistent
> fashion.
> >>
> >> Did you ever calculated something similar?
> >> If so, how?
> >> If not, any suggestion?
> >>
> >> Thanks in advance for all your comments.
> >>
> >> All the Best
> >>
> >> VG
> >>
> >> PS: Gromacs version: 5.0.4
> >>
> >> --
> >>
> >> ***********************************************************************
> >> *Vito Genna, Ph.D*
> >>
> >> *Postoctoral Researcher*
> >>
> >> *Molecular Modeling and Bioinformatics*
> >> *Orozco Lab*
> >>
> >> *Institute for Research in Biomedicine (IRB Barcelona)*
> >>
> >> *Parc Centific de Barcelona*
> >>
> >> *C/ Baldiri Reixac 10-12*
> >> *08028 Barcelona*
> >>
> >> ***********************************************************************
> >>
> >
> >
> >
> > --
> >
> > ***********************************************************************
> > *Vito Genna, Ph.D*
> >
> > *Postoctoral Researcher*
> >
> > *Molecular Modeling
> <https://maps.google.com/?q=*Molecular+Modeling&entry=gmail&source=g> and
> Bioinformatics*
> > *Orozco Lab*
> >
> > *Institute for Research in Biomedicine (IRB Barcelona)*
> >
> > *Parc Centific de Barcelona*
> >
> > *C/ Baldiri Reixac 10-12*
> > *08028 Barcelona*
> >
> > ***********************************************************************
> >
>
>
>
> --
>
> ***********************************************************************
> *Vito Genna, Ph.D*
>
> *Postoctoral Researcher*
>
> *Molecular Modeling and Bioinformatics*
> *Orozco Lab*
>
> *Institute for Research in Biomedicine (IRB Barcelona)*
>
> *Parc Centific de Barcelona*
>
> *C/ Baldiri Reixac 10-12*
> *08028 Barcelona*
>
> ***********************************************************************
> --
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