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2019/20 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 View Timetable

Year running 2019/20

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
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 typeNumberLength hoursStudent hours
Lecture111.0011.00
Practical111.0011.00
Private study hours128.00
Total Contact hours22.00
Total hours (100hr per 10 credits)150.00

Private study

128

Methods of assessment


Coursework
Assessment typeNotes% of formal assessment
ReportProposal for a simulation project including methods to be used and computer time requested (Approx 1000 words)50.00
Presentationshort 'project pitch' presentation20.00
Computer ExerciseSimulation skills15.00
Computer ExerciseSimulation skills15.00
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 module

Last updated: 08/03/2019

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