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.

THIS EXPERIMENTAL SCRIPT IS NOT YET COMPLETE

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 physics 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. INSTRUCTIONS FOR HOW TO PREPARE THIS. Your report should explain what you did in each stage of the experiment, and what your findings were. Each section of the experimental script gives some details about what your report should contain for that section.

Getting Help

Technical help with laptops (existing page) Workshop times / email contacts

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.

1. Running your first simulation
2. Introduction to molecular dynamics simulation
3. Equilibration
4. Running simulations under specific conditions
5. Calculating heat capacities using statistical physics Fluctuation formulae for $C_v,\ C_p$ (as appropriate). Effect of $N$
6. Structural properties and the radial distribution function $G\left(r\right)$ - coordination number? PMF?
7. Dynamical properties and the diffusion coefficient, GK vs NEMD