Molecular Dynamics

Let particles experience forces, accelerate, collide, and derive macroscopic phenomena from microscopic trajectories

Molecular dynamics doesn't directly prescribe "how temperature behaves"; instead, particles follow Newton's laws of motion. Forces determine acceleration, which updates velocity, which drives position. Macroscopic properties emerge from statistical analysis of these microscopic trajectories.

Particle Trajectory Interparticle Forces Energy Evolution Micro to Macro
Enter Interactive Lab

The key to MD is not just "looking like it moves"

What truly matters: each small step is governed by mechanical laws. Temperature, energy, and local structures are later derived from trajectory statistics.

Particles Each point represents a molecule or atom with position, velocity, and forces.
Forces Too close causes strong repulsion; moderate distances may attract. This determines whether structures aggregate.
Integration The system updates at tiny time steps. These small updates accumulate into complete trajectories.
Statistics Kinetic energy, potential energy, average velocity, and aggregation degree are macroscopic results derived from trajectories.
Understanding the Method

Molecular dynamics transforms "physical laws" into a sequence of tiny time steps

Once you can define interparticle forces, you can obtain particle trajectories through time integration. Temperature, energy, diffusion, and aggregation can then be statistically derived from these trajectories.

1

Initialize Particles

Set initial positions and velocities for particles. These are the starting points for system evolution, and different initial values lead to different transient behaviors.

2

Calculate Interparticle Forces

Interparticle forces typically depend on distance: strong repulsion at close range, weak attraction at moderate distances. This forms the basis for local structure formation.

3

Advance One Time Step

Update acceleration, velocity, and position based on forces. The time step must be sufficiently small to ensure simulation stability and reliability.

4

Compute Macroscopic Quantities

Kinetic energy, potential energy, average velocity, and aggregation degree are all system-level quantities statistically derived from numerous microscopic trajectories.

Teaching Experiment on This Page

We place a group of interacting particles in a 2D box. You can adjust temperature, attraction strength, and particle size to directly observe the transition from dispersed motion to aggregation.

Interactive Lab

Increase temperature, strengthen attraction, observe particle structure and energy change together

Brighter particle color indicates higher velocity. The curves below record both kinetic and potential energy changes, helping you connect "observed motion" with "measured energy".

2D Particle Box
This is the most intuitive microscopic view. Particles continuously experience forces and collisions; local interactions gradually accumulate into observable collective structures.
Lower Velocity Higher Velocity Enhanced Local Clustering
Energy Evolution Curve
Kinetic and potential energy continuously exchange based on particle arrangement. Understanding this curve elevates "motion observation" to "explanation capability".
How to Read Results
MD typically provides trajectories first, then derives thermodynamic quantities, diffusion behaviors, and structural metrics from them.

After the model starts evolving, explanations will be provided based on current energy and structural state.

When to Use

When you care about how microscopic interactions grow into macroscopic properties

Phase transitions, diffusion, interface behavior, cluster formation, nanostructures, and thermal motion often require understanding from the perspective of particle-level forces and motion.

①

You care about trajectories themselves

MD is ideal if you want to know how particles move, collide, and aggregate, rather than just final averages.

②

Mechanical laws are well-defined

As long as you can reasonably define inter-particle forces, you can advance system evolution through time integration.

③

Macroscopic quantities emerge from statistics

Temperature, energy, structure factors, diffusion coefficients, etc. are typically derived from microscopic trajectories rather than directly input.