[gmx-users] Energy decomposition

[Vito GENNA]

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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