Molecular Modelling


Many important things happen at scales so small and fast that we cannot see them with our own eyes or even with a conventional microscope. Computers allow us to model these atomic systems and gain important information needed to understand what is happening and use this knowledge to designing new materials! This is called a computational microscope because it uses computer simulations to look at things at a microscopic level.

Engineers have an exciting role as designers and modellers. Instead of simply looking at something and asking “Why is that like that?” or “Why does that happen?”, engineers ask “How can I make something useful with that?”. This involves understanding science and applying it to problems or challenges in real life. This is an exciting field full of opportunities using both traditional and innovative technologies.

Here we will explore molecular dynamics, a modelling method developed to apply fundamental chemistry and physics in a computer model that allows us to simulate and test phenomena and technologies.

Learning outcomes:
1. Identify fundamental factors to describe the movement of microscopic systems
2. Understand how molecular dynamics is able to model atomic behaviour

Let's look at atoms!

Atoms are the building blocks of the universe… Everything we see or taste or smell or touch is made up of atoms. We are made out of atoms!!

This means to fully understand matter and predict its behaviour and properties in different environments, we need to look at an atomic level.

Remember even though we can’t see them, molecules are always moving. Molecules bend, stretch, spin, and move through space. Atoms that are bonded together bounce back and forth like two balls attached by a spring. Here are some videos showing a water molecule (known chemically as H2O because it is made up of two hydrogen atoms bonded to one oxygen atom) rotating, bending, and stretching about its bonds.

This movement plays a big role in how a molecule interacts with its environment and this affects material properties.

Let’s think about some questions that can only be answered by looking at an atomic level.

Can you answer these questions about H2O by explaining the behaviour and interactions between atoms and molecules?

Question 1: Why does ice float?

The solid form of almost all matter is denser than its liquid form – but not water. Why does H2O in its solid form (ice) expand to take up more space than liquid water?

Sketch out an answer and try to explain it out loud.

Answer 1: Watch the first video below to hear the explanation at an atomic level 

Question 2: How many different types of ice are there?

Different types of ice can be categorised by the arrangement of H2O molecules. How many types do you think there are and can you predict their molecular arrangement(s)?

Try drawing the arrangements. Also think about what conditions might cause different types of ice to form.

Answer 2: Listen to the second video for the answers. 

And for fun, watch the next a video showing the molecular movement as crystalline ice melts!

Question 3: Why can water striders (and paper clips!) float on top of water, even though they are denser than the liquid?

Water has an amazing ability to hold things on its surface when you would expect them to sink. There is another video below showing great footage of this.

Describe the role of intermolecular interactions in explaining the surface tension of water.

Answer 3: There is another video with diagrams helping unpack the atomic insights into water surface tension.

Video Resource

Video Resource

Video Resource

Video Resource

Video Resource

Resource activities

Molecular Dynamics Simulations

How can we understand what is happening at an atomic or molecular scale? Learn more about how we model and simulate atoms.


Applications of Molecular Dynamics

Find out more about how molecular dynamics is used.


Reflective questions

To answer and record these questions you will need to have an account and be logged in.

Task 1

What are the key arguments, concepts, points contained within it?

Task 2

What are you struggling to understand?

What could you do to improve your understanding of these concepts/terminology etc.?

Task 3

What further questions has this resource raised for you?

What else are you keen to discover about this topic and how could you go about learning more?

Can you make any links between this topic and your prior knowledge or school studies?

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Further reading

  • Energy functions and their relationship to molecular conformation

    Lecture slides providing more details on molecular dynamic simulations

  • Atoms in Motion

    Explore molecular simulations through an interactive simulation (downloaded on app). The “Atoms In Motion” tab at the top has 5 pages providing helpful explanations atoms, gases, ions, salts, and molecular dynamics!


    Download the program SIMOLANT to see molecular dynamics in action!

  • Potential Energy Function

    Explanation about the motion of atomic systems and some details about how they are described in potential energy functions (called force fields!)