[gmx-users] Interaction energy, vdW and electrostatic

Justin Lemkul jalemkul at vt.edu
Thu Dec 13 13:33:21 CET 2018

On 12/13/18 3:27 AM, daniel madulu shadrack wrote:
> Hi all,
> I am simulating a polymer with drug (polymer-drug) complex, I want to plot
> the interaction energy. I use gmx energy -f xx.edr, I am getting a long
> list with kind of energy eg
> LJ-SR:polymer-polymer
> LJ-14:polymer-polymer
> LJ-SR:polymer-drug
> LJ-14:polymer-drug etc
> also I have
> Coul-SR:polymer-polymer
> Coul-14:polymer-polymer
> Coul-SR:polymer-drug
> Coul-14:polymer-drug etc
> So, is Coul-SR:polymer-drug stands for van der wall? and LJ-SR:polymer-drug
> stand for electrostaics?

You have it backwards. LJ = Lennard-Jones (van der Waals) and Coul = 
Coulombic (electrostatics).

> But when I use for example, LJ-14:polymer-drug I get zero, but when I use
> LJ-SR:polymer-drug I get -88.8 kJ/mol.

A 1-4 interaction is purely intramolecular, so all intermolecular 1-4 
terms are zero by definition.

> Is this -88 the total interaction energy? how do I get the vdW and
> electrostatic to get the total interaction energy?

No, that is the short-range LJ contribution to the interaction energy 
(hence LJ-SR). The total would be LJ-SR + Coul-SR. Whether this quantity 
has any physical meaning depends on the force field, but in most cases 
it is not a real, physically relevant quantity.



Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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