[gmx-users] Energy decomposition

[Vito GENNA]

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 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*

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