[gmx-users] Energy decomposition

Justin Lemkul jalemkul at vt.edu
Sun Jul 8 20:13:06 CEST 2018

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.


> 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


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