---
title: "Molecular dynamics · Library · Simulation Hypothesis"
url: https://simulation-hypothesis.com/library/molecular-dynamics
description: "Molecular dynamics is a way of simulating atoms and molecules on a computer."
license: https://creativecommons.org/licenses/by/4.0/
credit: "Ross Allan Dahl, Simulation Hypothesis (simulation-hypothesis.com)"
---

## Physics & computation

# Molecular dynamics

Definition

Molecular dynamics is a way of simulating atoms and molecules on a computer. It steps Newton’s equations forward with empirical force fields, usually in femtosecond timesteps. It’s the workhorse of computational chemistry.

On this site

The Atom rung uses the standard all-atom figure of about a thousand operations per atom per femtosecond step.

Role in the model

The Atom rung uses the operations per atom per femtosecond that chemists really use when they simulate a protein. The difference is scale. They simulate millions of atoms for microseconds. The sandbox asks for a whole planet over a century.

Related

[Matter fidelity](https://simulation-hypothesis.com/library/matter-fidelity)[Timestep](https://simulation-hypothesis.com/library/timestep)

In the trees

[Molecular dynamics · Simulations](https://simulation-hypothesis.com/trees/simulations?n=m-md)[Hard-sphere fluids · Simulations](https://simulation-hypothesis.com/trees/simulations?n=mat-hard)

## The people behind the terms

14 short pages, one per thinker, each with its matching dial. See also the [reading list](https://simulation-hypothesis.com/reading).

[Plato’s cave](https://simulation-hypothesis.com/thinkers/plato)[Zhuangzi’s butterfly](https://simulation-hypothesis.com/thinkers/zhuangzi)[Vasubandhu’s dream](https://simulation-hypothesis.com/thinkers/vasubandhu)[Shankara’s māyā](https://simulation-hypothesis.com/thinkers/shankara)[al-Ghazali’s doubt](https://simulation-hypothesis.com/thinkers/ghazali)[Ibn Arabi’s imagination](https://simulation-hypothesis.com/thinkers/ibn-arabi)[Calderón’s life is a dream](https://simulation-hypothesis.com/thinkers/calderon)[Descartes’ demon](https://simulation-hypothesis.com/thinkers/descartes)[Berkeley’s perceiver](https://simulation-hypothesis.com/thinkers/berkeley)[Borges’ circular ruins](https://simulation-hypothesis.com/thinkers/borges)[Nozick’s experience machine](https://simulation-hypothesis.com/thinkers/nozick)[Putnam’s brain in a vat](https://simulation-hypothesis.com/thinkers/putnam)[Bostrom’s trilemma](https://simulation-hypothesis.com/thinkers/bostrom)[Chalmers: virtual worlds are real](https://simulation-hypothesis.com/thinkers/chalmers)