[gmx-users] "energygrps" option for separating Bonded interactions

Justin Lemkul jalemkul at vt.edu
Fri May 18 22:09:29 CEST 2018

On 5/18/18 4:01 PM, Debdas Dhabal wrote:
> Dear all,
> I wonder if GROMACS has "energygrps" option (or any other similar options)
> for bonded interactions (E_bond, E_ang, E_dih) for different groups. Let's
> say I have three different chains in a single box and I want to extract the
> bonded interactions for every chain separately. Would I be able to do that
> on the fly during Gromacs run. I went through the webmanual and gmx_user
> page but didn't find any solution for that. I would be very grateful if
> someone could help me sharing how I could do this.

energygrps will do nothing for bonded terms.

If you want bonded energies of individual components, you will have to 
strip out the coordinates you want from the trajectory (trjconv), make a 
corresponding .tpr file (convert-tpr) and use mdrun -rerun to compute 
the potential energy of that species. Note that these quantities are 
quite unlikely to have any physical meaning.



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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