Third year simulation experiment

Liquid simulations: this is the optional experiment which may be chosen by any third year student.

If you are looking for the Programming-Ising experiment, you will find it here.

To run this experiment, you will need the molecular dynamics code LAMMPS. LAMMPS runs on laptops, desktop computers and supercomputers. You will be provided with access to a Microsoft Azure Lab Virtual Machines (VM), which has LAMMPS pre-installed.

Introduction

Computer simulation is widely used to study a huge variety of chemical phenomena, from the behaviour of materials and molecules under extreme conditions to protein folding and the properties of biological systems such as lipid membranes. In this experiment, we will give you an introduction to one of the most powerful methods for the simulation of chemical systems, molecular dynamics simulation.

We will begin with a brief overview of the fundamental theory behind the method, before you start running your own simulations of an atomistic liquid.

At the end of this experiment, you will have performed your own simulations with state of the art software packages used by researchers all around the world, and used those simulations to investigate thermophysical and structural properties of liquids, solids and gases. You will learn to compute thermodynamic quantities such as temperature and pressure.

All the information that you need to complete the experiment is provided in these wiki pages. We have provided 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.

You may find helpful revising the thermodynamic concepts in Solids, Liquids and Interfaces (2nd year lectures by Prof. Fernando Bresme).

Assessment

At the end of this experiment you must submit a report (pdf format via turnitin) and a zip file with inputs and outputs. The report should be structured:

Introduction Questions (20% of the total mark)
Results and Discussion (60% of total mark)
Conclusion Questions (20% of total mark)
References (see note below)

Relevant supplementary material can be added at the end of the report so long as it supports your discussion. Please limit the introduction and conclusion sections (which are now just answers to questions) to a maximum of ~1.5 pages at size 12 font Times New Roman, or equivalent (e.g. if you are using latex or simply prefer another font). It is certainly possible to answer the introduction and conclusion questions with under this length limit, and as with most scientific writing, shorter concise but well thought out answers are preferable. We have not imposed a hard word limit because, equally, you should spend the majority of this lab learning, not editing and rewriting answers to just satisfy the word limit.

Please note that five "floating" marks have been reserved in the results and discussion section. These can be used to reward particularly insightful comments and/or explanations, on the basis of good/bad presentation, use of scientific language, or for other reasons.

It is important to provide appropriate references. 'Appropriate' refers to both quality (books and peer-reviewed papers are preferred over a link to wikipedia) and quantity (make sure to include references where you used them, but there is no point quoting 10 papers for a statement like 'macroscopic systems consist of a large number of atoms'). Please note that presenting external information as your own counts as plagiarism! As a bare minimum, you will need to reference the information you present in your introduction.

Copy&Paste will not be accepted, even if referenced! Every report is automatically checked for plagiarism. If you copy paste text, this will be flagged up as plagiarised. Think carefully what you write, and use your own words and conclusions.

The final task of the lab (task 10 - MSD diffusion simulations) is NOT part of the lab. That section provides information on calculations of dynamic properties. If you are interested in learning more about simulations, please give it a go. However, you should NOT submit this material as part of your lab report, as it will not be marked.

Getting Help

The best approach to get help is to attend the Teams sessions. The demonstrators will be available to answer questions between 10-12 and 3-4 on Mon, Tue, Thu and Fri. Please feel free to contact the demonstrators via Teams, and ask for help during the lab sessions. Questions can also be asked via email.

The member of academic staff responsible for this exercise is Professor Fernando Bresme (f.bresme@imperial.ac.uk). Please feel free to contact Prof. Bresme via email if you have questions about the molecular dynamics method, the theoretical background behind molecular dynamics (statistical thermodynamics) or questions about the exercises.

Structure of this Experiment

This experimental manual has been broken up into a number of subsections. To help you plan your time it is suggested you complete the following at these times:

Monday (morning session): Theory - Introduction to molecular dynamics simulations

Monday (afternoon session): Theory + Equilibration (submit your files for running)

Tuesday (morning session): Equilibration (analyse your files)

Tuesday (afternoon session): Running simulations under specific conditions (submit and read)

Thursday (morning session): Checkpoint for progress. Submit your input files for the radial distribution function and analyse your equation of state from the previous section

Thursday (afternoon session).

Friday (morning session): Analyse MSD diffusion simulations - as noted above this exercise is not compulsory

Friday (afternoon session): Analyse MSD diffusion simulations. Report write-up.

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.

Introduction Questions

Please limit your answers to this section (which are now just answers to questions) to a maximum of ~1.5 pages at size 12 font Times New Roman, or equivalent (e.g. if you are using latex or simply prefer another font).

Give a brief account on what molecular dynamics is, and (broadly speaking) what it aims to achieve. [5]
Give two examples of instances where molecular dynamics simulations have/can be used (in a helpful way) instead of or in synergy with experimental techniques. In each case explain why. [10] (Please consider only chemically relevant examples. E.g. To study geochemical processes which occur under extreme temperature/pressure conditions, and therefore difficult to study experimentally.)
Computer simulations are performed under specific "experimental" conditions. The thermodynamic ensemble defines these conditions. Explain what is meant by the thermodynamic ensemble. Your answer should also provide three ensemble examples and briefly discuss what quantities are conserved in each ensemble. You may want to consult Atkins' Physical Chemistry 11th edition (Focus 13D) to address this question. [5]

Conclusion Questions

Please limit your answers to this section (which are now just answers to questions) to a maximum of ~1.5 pages at size 12 font Times New Roman, or equivalent (e.g. if you are using latex or simply prefer another font).

In this lab, you have used the Lennard-Jones potential exclusively. Give one example of a system that can be described well using only LJ potentials. What additional elements would you need to add to the interaction potential to model a molecule, e.g. water? [6]
What cut-off have you been using in your simulations? What are the advantages and disadvantages for using a shorter/longer cut-off? (Hint: consider here the balance of computational cost vs accuracy in describing the properties of a system.) [3]
In this lab you have investigated the properties of solids, liquids and gases. Would you observe a liquid phase (and by extension a critical point) if the LJ interaction strength, $ε$ , is very weak? What interaction strength is required to generate a liquid phase? (Hint: to address this question you may want to revise the 2nd year Solids, Liquid and Interfaces lecture notes - see "Phase transitions of pure substances") [4]
What are finite size effects? Do you think they are significant in the simulations you have performed? Why? [3]
Algorithms such as SHAKE and RATTLE are widely used to model molecular systems as they allow MD simulations to be performed while fixing bond lengths. Why is this desirable? [4] (Hint: think about the timestep.)