[gmx-users] Energy decomposition

[Mark Abraham]

Hi,

On Tue, Jul 24, 2018, 12:33 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?
>

No. What value would be appropriate, and why?

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?
>

You can edit the topology before you give it to grompp if the default
decomposition isn't suitable for you. But I know of no use for such a
decomposition, nor a force field that was parameterized with such a use
case in mind.

Mark

Thanks in advance for your contribute.
>
> V
>
> On Sun, Jul 8, 2018 at 8:17 PM, Vito GENNA <vito.genna at irbbarcelona.org>
> wrote:
>
> > Dear Justin,
> >
> > Thanks a lot.
> > I indeed did not consider the idea to extrapolate only a part of the
> whole
> > trajectory. Nice shot.
> > Well, regarding the forcefield, this calculation in part is aiming to a
> > kind of “ff validation”.
> >
> > Thanks a lot for your prompt reply.
> >
> > V
> >
> > *Vito Genna, Ph.D*
> > PostDoctoral Researcher
> > Molecular Modelling and Bioinformatics
> > Orozco Lab
> >
> > *Dep. of Structural and Computational Biology*
> > *Institute for Research in Biomedicine (IRB Barcelona)*
> > Parc Científic de
> <https://maps.google.com/?q=Parc+Cient%C3%ADfic+de+&entry=gmail&source=g>
> Barcelona
> > C/ Baldiri Reixac 10-12
> > 08028 Barcelona
> >
> > P.S. This message has been written with my IPhone. Sorry for typo.
> >
> > Il giorno 08 lug 2018, alle ore 20:12, Justin Lemkul <jalemkul at vt.edu>
> ha
> > scritto:
> >
> >
> >
> > On 7/8/18 2:06 PM, Vito GENNA 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?
> >
> >
> > You need to extract only the coordinates you want from the trajectory
> with
> > trjconv and your index group. Then, create a matching .tpr file with only
> > those atoms using convert-tpr. Then use mdrun -rerun. Whether or not the
> > quantity means anything depends on how your force field was parametrized,
> > but that's how you calculate it.
> >
> > -Justin
> >
> > If not, any suggestion?
> >
> >
> > Thanks in advance for all your comments.
> >
> >
> > All the Best
> >
> >
> > VG
> >
> >
> > PS: Gromacs version: 5.0.4
> >
> >
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Virginia Tech Department of Biochemistry
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.thelemkullab.com
> >
> > ==================================================
> >
> > --
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> >
>
>
> --
>
> ***********************************************************************
> *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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