2017/18 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 2017/18

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 Monte Carlo and using maple to write simulation code for Lennard Jones (LJ) particles.
- Introduction to Molecular Dynamics (MD) simulations and using maple to write a basic MD code for LJ particles.
- Thermostats, barostats and periodic boundary conditions.
- Setting up a simulation using AMBER or NAMD or GROMACS.
- Forcefields and atom types.
- 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
Lecture	11	1.00	11.00
Practical	11	1.00	11.00
Private study hours			128.00
Total Contact hours			22.00
Total hours (100hr per 10 credits)			150.00

Private study

128

Methods of assessment

Coursework

Assessment type	Notes	% of formal assessment
Report	Proposal for a simulation project including methods to be used and computer time requested (Approx 1000 words)	50.00
Presentation	short 'project pitch' presentation	20.00
Computer Exercise	Simulation skills	15.00
Computer Exercise	Simulation skills	15.00
Total percentage (Assessment Coursework)		100.00

Normally resits will be assessed by the same methodology as the first attempt, unless otherwise stated

Reading list

There is no reading list for this module

Last updated: 23/03/2018

Disclaimer

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