[gmx-users] gmx enenrgy

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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