2023/24 Undergraduate Module Catalogue

PHYS3190 Molecular Simulation: Theory and Practice

15 creditsClass Size: 60

Module manager: Dr Ben Hanson
Email: b.s.hanson@leeds.ac.uk

Taught: Semester 2 (Jan to Jun) View Timetable

Year running 2023/24

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.

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
Students will be able to demonstrate knowledge, understanding and application of:

- The theoretical background to materials simulation.
- The use of high performance computing in material science.
- The practical limitations of computer simulation.
- The use of research simulation software

Students will also demonstrate the ability to:

- Manage time and plan work to meet deadlines

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
Independent online learning hours			3.00
Private study hours			114.00
Total Contact hours			33.00
Total hours (100hr per 10 credits)			150.00

Methods of assessment

Coursework

Assessment type	Notes	% of formal assessment
Assignment	Grant Exercise	40.00
Computer Exercise	Python Exercise	40.00
Computer Exercise	Simulation Exercise	20.00
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: 05/01/2024

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