2021/22 Undergraduate Module Catalogue
PHYS3190 Molecular Simulation: Theory and Practice
15 creditsClass Size: 60
Module manager: Dr Sarah Harris
Email: S.A.Harris@leeds.ac.uk
Taught: Semester 2 (Jan to Jun) View Timetable
Year running 2021/22
Pre-requisite qualifications
Prior knowledge of thermodynamics, statistical physics and chemical bonding would be an advantage.Module replaces
PHYS3170 Introductary Molecular SimulationThis 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.Objectives
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.
Syllabus
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 type | Number | Length hours | Student hours |
Workshop | 11 | 2.00 | 22.00 |
Lecture | 11 | 1.00 | 11.00 |
Private study hours | 117.00 | ||
Total Contact hours | 33.00 | ||
Total hours (100hr per 10 credits) | 150.00 |
Methods of assessment
Coursework
Assessment type | Notes | % of formal assessment |
Computer Exercise | Computer Exercises | 60.00 |
Computer Exercise | Grant Exercise | 40.00 |
Total percentage (Assessment Coursework) | 100.00 |
Students are required to submit all elements of the coursework in order to pass the module.
Reading list
There is no reading list for this moduleLast updated: 12/07/2021 13:47:39
Browse Other Catalogues
- Undergraduate module catalogue
- Taught Postgraduate module catalogue
- Undergraduate programme catalogue
- Taught Postgraduate programme catalogue
Errors, omissions, failed links etc should be notified to the Catalogue Team.PROD