Lennard-Jones Potential

In many areas of computational chemistry, physics, and mathematics, the Lennard-Jones

potential is a semi-empirical model that describes the motion of a particle. It was first studied by
John Lennard-Jones in 1924 (Wikipedia, 2015). The equation of Lennard-Jones potential is

𝑟𝑚 12 𝑟𝑚 6
𝑉(𝑟) = 𝜀 [( ) − 2( ) ] ,
𝑟 𝑟

where 𝜀 is depth of potential well.

𝑟𝑚 is potential at which the distance between two particles is minimum.

𝑟 is distance between two particles.

By plotting its parameters, we will obtain the following graph.

𝑉(𝑟)

𝑟𝑚

Figure 1.1 : A graph of Lennard-Jones potential

1
What makes the graph having this attribute?

It is fundamentally based on the summation of two potential equations in which are

𝑚 𝑟
Positive potential : + 𝑟 12

𝑟
Negative potential : − 𝑟𝑚6

Plotting two graphs at the same time,

𝑉(𝑟)
𝑟𝑚
+ 𝑟 12

𝑟
− 𝑟𝑚6

Figure 6.2 : A graph of positive potential and negative potential.

In other words, the Lennard-Jones potential equation is fundamentally based on the combination
of attractive and repulsive force. If we combine both equations, we will get the graph just like as
shown on figure 6.1. We shall analyse the figure 6.1 and observe what will happen to particles if
they are at certain distance 𝑟.

2
At 𝑟 < 𝑟𝑚 , two particles are so close to each other that repulsive force is taking over attractive
force just as shown below.

At 𝑟 = 𝑟𝑚 , two particles are touching each other. However, repulsive force becomes the
dominant force for them to repel.

At 𝑟 > 𝑟𝑚 , two particles are moving away from each due to their repulsive force. Nevertheless,
attractive force is taking over repulsive force for the particles to come back.

3
Since Lennard Jones potential naturally describes particle in motion, we can apply calculus of
variations and analytical mechanics to derive motion of particles constrained by Lennard-Jones
potential.

We shall use Lagrangian and Hamiltonian to describe its motion (Fowles and Cassiday, 2005).

𝐿 = 𝐾 − 𝑈,

1 2 2 2 2)
(𝑟𝑚 )12 2(𝑟𝑚 )6
= 𝑚(𝑥̇ 1 + 𝑥̇ 2 + 𝑦̇ 1 + 𝑦̇ 1 − 𝜀 [ − ].
2 ((𝑥2 − 𝑥1 )2 + (𝑦2 − 𝑦1 )2 )6 ((𝑥2 − 𝑥1 )2 + (𝑦2 − 𝑦1 )2 )3

Converting velocities into momenta,

𝜕𝐿 𝜕𝐿 𝜕𝐿 𝜕𝐿
= 𝑚𝑥̇ 1 = 𝑝𝑥1 , = 𝑚𝑥̇ 2 = 𝑝𝑥2 , = 𝑚𝑦̇ 1 = 𝑝𝑦1 , = 𝑚𝑦̇ 2 = 𝑝𝑦2 ,
𝜕𝑥̇ 1 𝜕𝑥̇ 2 𝜕𝑦̇ 1 𝜕𝑦̇ 2

So in Hamiltonian,

𝐻(𝑝𝑥1 , 𝑝𝑥2 , 𝑝𝑦1 , 𝑝𝑦2 , 𝑥1 , 𝑥2 , 𝑦1 , 𝑦2 )

1
= (𝑝𝑥21 + 𝑝𝑥22 + 𝑝𝑦21 + 𝑝𝑦22 )
2𝑚
(𝑟𝑚 )12 (𝑟𝑚 )6
+𝜀[ − ],
((𝑥2 − 𝑥1 )2 + (𝑦2 − 𝑦1 )2 )6 ((𝑥2 − 𝑥1 )2 + (𝑦2 − 𝑦1 )2 )3

𝜕𝐻 𝑝𝑥 𝜕𝐻 12(𝑟𝑚 )12 (𝑥2 − 𝑥1 ) 12(𝑟𝑚 )6 (𝑥2 − 𝑥1 )

= 1 = 𝑥̇ 1 , = 𝜀 [− + ],
𝜕𝑝𝑥1 𝑚 𝜕𝑥1 ((𝑥2 − 𝑥1 )2 + (𝑦2 − 𝑦1 )2 )7 ((𝑥2 − 𝑥1 )2 + (𝑦2 − 𝑦1 )2 )4

𝜕𝐻 𝑝𝑥 𝜕𝐻 12(𝑟𝑚 )12 (𝑥1 − 𝑥2 ) 12(𝑟𝑚 )6 (𝑥1 − 𝑥2 )

= 2 = 𝑥̇ 2 , = 𝜀 [− + ],
𝜕𝑝𝑥2 𝑚 𝜕𝑥2 ((𝑥2 − 𝑥1 )2 + (𝑦2 − 𝑦1 )2 )7 ((𝑥2 − 𝑥1 )2 + (𝑦2 − 𝑦1 )2 )4

𝜕𝐻 𝑝𝑦 𝜕𝐻 12(𝑟𝑚 )12 (𝑦2 − 𝑦1 ) 12(𝑟𝑚 )6 (𝑦2 − 𝑦1 )

= 1 = 𝑦̇ 1 , = 𝜀 [− + ],
𝜕𝑝𝑦1 𝑚 𝜕𝑦1 ((𝑥2 − 𝑥1 )2 + (𝑦2 − 𝑦1 )2 )7 ((𝑥2 − 𝑥1 )2 + (𝑦2 − 𝑦1 )2 )4

𝜕𝐻 𝑝𝑦 𝜕𝐻 12(𝑟𝑚 )12 (𝑦1 − 𝑦2 ) 12(𝑟𝑚 )6 (𝑦1 − 𝑦2 )

= 1 = 𝑦̇1 , = 𝜀 [− 7
+ ],
𝜕𝑝𝑦1 𝑚 𝜕𝑦2 2 2 4
((𝑥2 − 𝑥1 )2 + (𝑦2 − 𝑦1 ) ) ((𝑥2 − 𝑥1 )2 + (𝑦2 − 𝑦1 ) )

4
 𝜕𝐻 𝜕𝐻
𝑝̇𝑥1 = − = 𝑚𝑥̈ 1 , 𝑝̇𝑦1 = − = 𝑚𝑦̈ 1 ,
𝜕𝑥1 𝜕𝑦1

𝜕𝐻 𝜕𝐻
𝑝̇𝑥2 = − = 𝑚𝑥̈ 2 , 𝑝̇𝑦2 = − = 𝑚𝑦̈ 2 ,
𝜕𝑥2 𝜕𝑦2

Therefore, the equations of motion are

12(𝑟𝑚 )12 (𝑥2 − 𝑥1 ) 12(𝑟𝑚 )6 (𝑥2 − 𝑥1 )

𝑚𝑥̈ 1 = 𝜀 [− + ],
((𝑥2 − 𝑥1 )2 + (𝑦2 − 𝑦1 )2 )7 ((𝑥2 − 𝑥1 )2 + (𝑦2 − 𝑦1 )2 )4

12(𝑟𝑚 )12 (𝑥1 − 𝑥2 ) 12(𝑟𝑚 )6 (𝑥1 − 𝑥2 )

𝑚𝑥̈ 2 = 𝜀 [− + ],
((𝑥2 − 𝑥1 )2 + (𝑦2 − 𝑦1 )2 )7 ((𝑥2 − 𝑥1 )2 + (𝑦2 − 𝑦1 )2 )4

12(𝑟𝑚 )12 (𝑦2 − 𝑦1 ) 12(𝑟𝑚 )6 (𝑦2 − 𝑦1 )

𝑚𝑦̈ 1 = 𝜀 [− + ],
((𝑥2 − 𝑥1 )2 + (𝑦2 − 𝑦1 )2 )7 ((𝑥2 − 𝑥1 )2 + (𝑦2 − 𝑦1 )2 )4

12(𝑟𝑚 )12 (𝑦1 − 𝑦2 ) 12(𝑟𝑚 )6 (𝑦1 − 𝑦2 )

𝑚𝑦̈ 2 = 𝜀 [− + ].
((𝑥2 − 𝑥1 )2 + (𝑦2 − 𝑦1 )2 )7 ((𝑥2 − 𝑥1 )2 + (𝑦2 − 𝑦1 )2 )4

Its initial conditions are 𝑥1 (0) = 𝑥1 , 𝑥2 (0) = 𝑥2 , 𝑥̇ 1 (0) = 𝑥̇ 1 , 𝑥̇ 2 (0) = 𝑥̇ 2 , 𝑦1 (0) = 𝑦1 , 𝑦2 (0) =
𝑦2 , 𝑦̇ 1 (0) = 𝑦̇ 1 , 𝑦̇ 2 (0) = 𝑦̇ 2 . We would like to simplify the equations further by reducing to
system of first-order ordinary differential equations and use simple values. We shall let 𝑚 =
1, 𝜀 = 2, and 𝑟𝑚 = 1,

𝑢3 = 𝑥2 , 𝑢1 = 𝑥1 , 𝑣1 = 𝑦1 , 𝑣3 = 𝑦2 ,

𝑢4 = 𝑥̇ 2 , 𝑢2 = 𝑥̇ 1 , 𝑣2 = 𝑦̇ 1 , 𝑣2 = 𝑦̇ 1 ,

𝑢4 = 𝑥̈ 2 , 𝑢̇ 2 = 𝑥̈ 1 , 𝑣̇ 2 = 𝑦̈ 1 , 𝑣̇4 = 𝑦̈ 2 .

𝑢̇ 1 = 𝑢2 ,

24(𝑢3 − 𝑢1 ) 24(𝑢3 − 𝑢1 )
𝑢̇ 2 = − + ,
((𝑢3 − 𝑢1 )2 + (𝑣3 − 𝑣1 )2 )7 ((𝑢3 − 𝑢1 )2 + (𝑣3 − 𝑣1 )2 )4

𝑢̇ 3 = 𝑢4 ,

24(−𝑢3 + 𝑢1 ) 24(−𝑢3 + 𝑢1 )
𝑢̇ 4 = − 2 2 7
+ ,
((𝑢3 − 𝑢1 ) + (𝑣3 − 𝑣1 ) ) ((𝑢3 − 𝑢1 )2 + (𝑣3 − 𝑣1 )2 )4
 𝑣̇ 1 = 𝑣2 ,

24(𝑣3 − 𝑣1 ) 24(𝑣3 − 𝑣1 )
𝑣̇ 2 = − + ,
((𝑢3 − 𝑢1 )2 + (𝑣3 − 𝑣1 )2 )7 ((𝑢3 − 𝑢1 )2 + (𝑣3 − 𝑣1 )2 )4

𝑣̇ 3 = 𝑣4 ,

24(−𝑣3 + 𝑣1 ) 24(−𝑣3 + 𝑣1 )
𝑣̇4 = − + .
((𝑢3 − 𝑢1 )2 + (𝑣3 − 𝑣1 )2 )7 ((𝑢3 − 𝑢1 )2 + (𝑣3 − 𝑣1 )2 )4

Then, the initial conditions will be

𝑢1 (0) = 𝑢1 , 𝑢2 (0) = 𝑢2 , 𝑢3 (0) = 𝑢3 , 𝑢4 (0) = 𝑢4 ,

𝑣1 (0) = 𝑣1 , 𝑣2 (0) = 𝑣2 , 𝑣3 (0) = 𝑣3 , 𝑣4 (0) = 𝑣4 .