Re: [AMBER] Issue Lennard jones interaction

From: Jason Swails <>
Date: Sat, 13 Jun 2015 07:02:20 -0400

On Sat, Jun 13, 2015 at 5:01 AM, Loic ETHEVE <> wrote:

> Hi all,
> I encounter an issue when i do energy calculation between water and
> amino acid/dna.
> In general it affects negative amino acid (ASP/GLU). For these residus,
> lennard jones energy is often positive (between 2 and 6 kcal/mol) and
> electrostatic is very favorable so there is a physic issue with water
> molecules.
> Some of my colleague observe the same phenomenon using Gromacs.
> Does someone observe that or is this phenomenon already know in force
> field ?

​What makes you think this is a problem? All that matters is the *total*
energy. Recall that van der Waals interactions are highly repulsive at
short distances, since the electron clouds start overlapping and clashing
with each other, while they're attractive at larger distances (due to the
stabilizing effect of electron correlation).
​ The point in the Lennard-Jones potential where the potential energy
function goes from positive to negative is the "sigma" parameter.

​The way force fields work is by balancing out each others' effects. If
your electrostatic interaction is very attractive (as it would be between
oppositely-charged species, like water-hydrogen atoms with an ASP/GLU
carboxylate group), then the van der Waals term is necessary to keep them
from collapsing on top of one another (so the vdW energies may very well be

In nonpolar systems, however, the L-J potential is often negative, since
that's the primary form of attraction between the different atoms.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Sat Jun 13 2015 - 04:30:02 PDT
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