What is the Lennard-Jones potential?

V(r) = 4ε[(σ/r)¹² − (σ/r)⁶]. The r⁻¹² repulsive term models electron-cloud overlap; the r⁻⁶ attractive term models dispersion (van der Waals) forces. In reduced units ε=σ=1.

How do gas, liquid and solid phases differ in this simulation?

At high kT (>1.5) particles move freely with no structural order (gas). At medium kT (0.5-1.2) density-dependent local order forms (liquid). At low kT (<0.4) particles lock into a close-packed hexagonal lattice (solid).

What is velocity-Verlet integration?

A symplectic integrator: v(t+½dt) = v(t) + ½dt·F(t), then x(t+dt) = x(t) + dt·v(t+½dt), then compute F(t+dt) and complete v(t+dt). It conserves energy better than simple Euler integration.

What is the Berendsen thermostat?

A velocity-rescaling thermostat that gently nudges the system towards the target temperature T₀ by scaling velocities every τ steps by √[1 + (dt/τ)(T₀/T−1)]. It maintains temperature without disrupting dynamics.

Home▸Molecular Biology▸Lennard-Jones Molecular Dynamics — Interactive Particle Simulation

🧪 Lennard-Jones Molecular Dynamics — Interactive Particle Simulation

Simulate N-body Lennard-Jones molecular dynamics in 2D. Watch gas, liquid and solid phase transitions emerge from pairwise potentials. Velocity-Verlet integration, Berendsen thermostat, Maxwell-Boltzmann speed distributions.

Molecular Biology2DModerate60 FPS

⚙ Under the hood

This simulation models a system of Lennard-Jones particles using molecular dynamics. Users can observe the interactions between particles, including attractive and repulsive forces, leading to phenomena like crystallization and phase transitions.

Lennard-JonesMolecular DynamicsParticles

2D · HTML5 Canvas 2D · 60 FPS target · runs fully client-side, no install