Third year simulation experiment
This is the optional experiment which may be chosen by any third year student. If you are looking for the compulsory simulation experiment for students studying chemistry with molecular physics, you will find it here.
Introduction
Computer simulation is widely used to study a huge variety of chemical phenomena, from the behaviour of exotic materials under extreme conditions to protein folding and the properties of biological systems such as lipid membranes. In this experiment, we hope to give you a gentle introduction to one of the most powerful methods for the simulation of chemical systems, molecular dynamics simulation.
This course closely follows some of the ideas introduced in Professor Bresme's statistical thermodynamics lecture course. Do not worry if you are doing this experiment before the lectures begin, everything that you need to know to complete the experiment will be explained in these instructions. We will begin with a brief overview of the fundamental theory behind the method, before you start running your own simulations of a simple liquid using the college's high performance computing facilities.
At the end of this experiment, you will have performed your own simulations using state of the art software packages used by researchers all around the world, and used those simulations to calculate both structural and dynamic properties of a simple liquid. You will have seen how the concepts of statistical physics introduced by Professor Bresme are needed to calculate thermodynamic quantities such as temperature and pressure in computer simulations, and you will see how computers can be used to validate those concepts.
All of the information that you need to complete the experiment is provided in these wiki pages. We have also tried to provide links to external resources and relevant textbooks where possible — unless explicitly stated, reading these resources is not required; they are provided only as further information for those interested in the subject.
Assessment
At the end of this experiment you must submit a "report" in wiki form. You can find instructions on how to create the wiki page and edit it in the "Report Preparation" section of this page. Each section of the experiment has a number of tasks that you should complete, labelled TASK. If this is a mathematical exercise, your report should contain a short summary of the solution. If it is a graphical exercise, you should include the relevant image. Your report should explain briefly what you did in each stage of the experiment, and what your findings were. At the end of the experiment, you should send the link to your wiki report to n.jackson12@imperial.ac.uk.
YOU MUST SUBMIT YOUR WIKI REPORT BY 12 NOON ON THE FINAL FRIDAY OF THE EXPERIMENT.
Getting Help
For help with the chemistry department laptops, visit Mod:laptop.
Remember that if you take a college laptop, you MUST return it between 12 and 1pm on the final Friday of the experiment.
The demonstrator and assessor for this exercise is Niall Jackson (n.jackson12@imperial.ac.uk). He will be available in the second floor chemistry computer room between 1pm and 3pm on the first Monday of the experiment, and between 2pm and 3pm every other day. If you have questions outside of these times, you are of course welcome to send them by e-mail. The computational teaching fellow, Joao Bettencourt Cepeda Malhado (malhado@imperial.ac.uk), will be available in the same location between 1pm and 2pm daily.
The member of academic staff responsible for this exercise is Professor Fernando Bresme (f.bresme@imperial.ac.uk).
Structure of this Experiment
This experimental manual has been broken up into a number of subsections. Direct links to each of them may be found below. You should attempt them in order, and you should complete all of them to finish the experiment.
