New to LAMMPS? A Beginner's Guide to Molecular Dynamics

Molecular dynamics (MD) simulates how atoms move. You place atoms in a box, choose a model for the forces between them (the interatomic potential), and then step Newton’s equations of motion forward in time, a fraction of a femtosecond per step. From those trajectories you can measure things like temperature, pressure, structure, wetting, and heat flow.

The hardest part for most beginners isn’t the physics; it’s getting the first structure built and the first simulation running. This guide focuses on exactly that.

This guide was converted from my lecture materials into a website by AI. How it was made ↓

Who this is for

Students and researchers who have heard of MD and want to run it, but have never written a LAMMPS input script. You don’t need any programming experience. If you can edit a text file and type a command into a terminal, you can follow along.

What you will build

Chapter 1 Anatomy of an input script Every script in this guide shares the same skeleton. Learn it once here, then each later chapter only has to explain what is new. Chapter 2 Graphene Build a graphene sheet atom by atom with LAMMPS's own lattice, region and create_atoms commands, then run it at room temperature. Chapter 3 Silicon For common crystals you don't need to write the lattice yourself. Download the unit cell from Materials Project, build a supercell in OVITO, and load it with read_data. Chapter 4 hBN–stanene bilayer Stack a buckled stanene sheet on hexagonal boron nitride. Assign different atom types to different basis atoms, build a non-flat lattice, and combine several potentials in one simulation. Chapter 5 Carbon nanotube Build a graphene sheet, then roll it into a nanotube by moving every atom with a coordinate transformation, using LAMMPS loops and displace_atoms. Chapter 6 Droplet on a surface Place a liquid argon droplet on a copper plate surrounded by argon vapor, and watch it settle into its equilibrium shape. A first look at wetting and contact angles. Chapter 7 Running on a cluster When a simulation outgrows your laptop: log in to a cluster, move your files over, write a job script, submit it, and check on it, using only a handful of commands. Chapter 8 Try it yourself A practice problem that uses everything from the guide: build a thin film of liquid argon trapped between two copper walls, run it, and check it in OVITO.

Each system introduces a few new ideas, so it’s best to go in order. Every chapter follows the same pattern: what we are building, the idea behind it, the commands that are new, how to run and visualize it, and a few things to try on your own.

Before you start

You need three free programs:

Software	What it does	Get it
LAMMPS	The MD simulator that reads your input script and runs the simulation	lammps.org (Windows installers, conda, or build from source)
OVITO	Visualizes the atoms, makes images and movies, and can convert file formats	ovito.org (the free Basic version is enough)
A text editor	For writing input scripts	Any editor works; VS Code is a comfortable choice

Other tools you may come across: VMD (visualization), Avogadro (graphical structure builder), Atomsk and EMC (command-line structure builders), and commercial packages such as Materials Studio and MedeA.

Download the scripts with the All scripts button above. Each system is in its own folder, together with the potential file it needs.

About this guide

This guide is based on a two-part guest lecture I delivered in MAE 720: Molecular Level Modeling for Engineering Applications at North Carolina State University in Fall 2025.

The lecture and its materials are my own: the slides, the code notes, the LAMMPS input scripts, and the simulation movies. Converting these lecture materials into this website was done by AI. Working from the lecture recording’s transcript, the slides, the code notes and the scripts, the AI wrote the chapter text and drew the diagrams. The scripts on this site are the same as in the code notes, and each one was run in LAMMPS to check that it works. The written explanations may still contain minor mistakes.

If you spot an error or something unclear, please let me know.