2024/25 Undergraduate Module Catalogue

PHYS3190 Molecular Simulation: Theory and Practice

15 creditsClass Size: 70

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

Taught: Semester 2 (Jan to Jun) View Timetable

Year running 2024/25

Pre-requisite qualifications

A basic understanding of thermodynamics, statistical mechanics and Python programming is required.

Module replaces

PHYS3170 Introductary Molecular Simulation

This module is not approved as a discovery module

Module summary

Statistical mechanics is the basis of many theories in natural sciences and engineering and plays a prominent role in almost every branch of the subject. In your previous studies of statistical mechanics and thermodynamics, you may recall that thermodynamics can be derived from the statistical mechanics of molecules; from a knowledge of the energy levels available to a system of molecules. Up to this point we have made several assumptions that have enabled us to perform analytical calculations as part of our studies, restricting our analysis to simple systems like the ideal gas. However, computers open the way for us to consider specific, real and much more complicated systems of interacting molecules. In this module, we will guide you through two different (but complementary) types of simulation that allow us to study complex systems of interacting particles.In particular, the module will provide an introduction to the theory and practical implementation of Monte Carlo and Molecular Dynamics simulations of materials, including biomolecules, and will also provide practical experience of using standard software packages to perform these simulations on high performance computing facilities. In the lectures and practical sessions we will discuss the use of these simulations to calculate macroscopic properties from the microscopic properties of interacting molecules. We will apply Monte Carlo simulations to calculate the equation of state of Lennard Jones Gas, thermodynamic quantities of the harmonic oscillator to model chemical bonds, the magnetic properties of metallic solids, and the spread disease. We will then use the Lennard-Jones gas model to investigate the computational design of a bespoke Molecular Dynamics simulation designed specifically for this course. You will then use GROMACS to apply your knowledge to the simulation of complex biomolecules, and analyse these simulations to determine their physical properties.

Objectives

To develop a (bottom-up) 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 computational implementation of 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
- Usage of simulation methods to calculate macroscopic properties
- Basics of molecular simulation e.g. thermostats, barostats and periodic boundary conditions; forcefields and atom types.
- Computational investigation of molecular dynamics methods
- Setting up a simulation using AMBER or NAMD or GROMACS.
- Running an MD simulation on a supercomputer.
- Visualisation and basic data analysis (rmds, distances between atoms, angles, etc).
- Advanced topics (e.g. free energy, steered MD, metadynamics).
- Software carpentry.

- 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
In-course Assessment	Assessed Coursework	100.00
Total percentage (Assessment Coursework)		100.00

Students must submit a serious attempt at all assessments, in order to pass the module overall. There will be between 5 and 10 exercise sheets, each relating to an aspect of the course. Each exercise sheet will be equally weighted and the total will sum to 100% of the module mark. Exercise sheets will take the form of guided tasks, which will ask you to develop, perform and analyse simulations that you have learned about in the previous weeks of the module.

Reading list

There is no reading list for this module

Last updated: 14/10/2024

Disclaimer

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