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2022/23 Undergraduate Module Catalogue

PHYS3190 Molecular Simulation: Theory and Practice

15 creditsClass Size: 60

Module manager: Dr Sarah Harris

Taught: Semester 2 (Jan to Jun) View Timetable

Year running 2022/23

Pre-requisite qualifications

Prior knowledge of thermodynamics, statistical physics and chemical bonding would be an advantage.

Module replaces

PHYS3170 Introductary Molecular Simulation

This module is approved as a discovery module

Module summary

The module will provide an introduction to the theory of molecular dynamics and Monte Carlo simulations of materials, including biomolecules, and will provide practical experience of using standard software packages to perform these simulations on high performance computing facilities. The module will provide insight into the use of computing simulation in industry and engineering.


To provide an understanding of the methods used to simulate materials at the molecular level, and hands on experience of using the software.

Learning outcomes
An understanding of the theoretical background to materials simulation.
Practical experience of using research simulation software.
Understanding of the use of high performance computing in material science.
An understanding of the practical limitations of computer simulation.


22 sessions (mixture of lectures and practical classes).

- Introduction to computer simulations-motivation and applications.
- Introduction to numerical simulation methods using Python
- Basics of molecular simulation e.g. thermostats, barostants and periodic boundary conditions; forcefields and atom types.
- Setting up a simulation using AMBER or NAMD or GROMACS.
- Running an MD simulation on a supercomputer.
- Visulisation and basic data analysis (rmds, distances between atoms, angles, etc).
- Advanced topics (eg free energy, steered MD, metadynamics).
- Software carpentry.
- Research topic.

Teaching methods

Delivery typeNumberLength hoursStudent hours
Independent online learning hours3.00
Private study hours114.00
Total Contact hours33.00
Total hours (100hr per 10 credits)150.00

Methods of assessment

Assessment typeNotes% of formal assessment
AssignmentGrant Exercise40.00
Computer ExercisePython40.00
Computer ExerciseMD Practical20.00
Total percentage (Assessment Coursework)100.00

Students must submit a serious attempt at all assessments, in order to pass the module overall.

Reading list

There is no reading list for this module

Last updated: 29/04/2022 15:31:38


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