[gmx-users] Energy decomposition

Vito GENNA vito.genna at irbbarcelona.org
Sun Jul 8 20:06:10 CEST 2018

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

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


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*


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