[gmx-users] gmx enenrgy

Justin Lemkul jalemkul at vt.edu
Thu Jan 18 13:41:40 CET 2018

On 1/18/18 12:38 AM, kordzadeh at aut.ac.ir wrote:
> Hi all
> when we use "gmx energy" what is the difference between LJ-(SR), LJ-14, Coulomb-14, Coulomb(SR)?
> those mentioned energies, give us energy interaction of total system. right?

Not necessarily, because there may be long-range terms from PME or 
dispersion correction.

> if I want to determine interaction enenrgy for example, LJ, between two special species, not in total system, what should I do?

Define energygrps in the .mdp file and re-evaluate the energies of the 
trajectory with mdrun -rerun. Note that for most force fields, this 
value has no physical significance.



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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