[gmx-users] Energy decomposition

[Vito GENNA]

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 8:17 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 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*

***********************************************************************