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.

To run this experiment, you will need access to the Imperial College supercomputers. If you have VPN installed, you should be able to access the computers directly.

If you have not yet installed VPN, you may 1) use Remote Desktop connection (VPN not needed) or 2) install VPN.

Please follow the instructions to use one of these two options:

A) Remote Desktop connection

B) using VPN

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 (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

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.

The final task of the lab (task 10 - MSD diffusion simulations) is NOT part of the lab this year. The section has been left on the wiki for any interested student to give it a go. However, it should NOT be submitted as part of your lab report, and will not be marked.

Getting Help

Please feel free to ask any demonstrators for help during the lab sessions - that is what we are here for. 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).

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

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.

1. Downloading the Files
2. Introduction to molecular dynamics simulation
3. Equilibration
4. Running simulations under specific conditions
5. Structural properties and the radial distribution function
6. Dynamical properties and the diffusion coefficient

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).

1. Give a brief account on what molecular dynamics is, and (broadly speaking) what it aims to achieve. [5]
2. 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 cannot be studied experimentally.)
3. Explain what is meant by a thermodynamic ensemble, and the term "conserved quantity". [2]
4. What is the Ergodic hypothesis? Explain its relevance to molecular dynamics simulations. [3]

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).

1. 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, and one that cannot. In each case explain why. [4]
2. What cut-off have you been using in your simulations? What are the advantages and disadvantages for using a shorter/longer cut-off? [3]
3. What are finite size effects? Do you think they are significant in the simulations you have performed? Why? [3]
4. Algorithms such as SHAKE and RATTLE (holonomic constraints) allow MD simulations to be performed while fixing bond lengths. Why is this desirable? [3] (Hint: think about the timestep.)
5. In the simulations you have performed ergodicity has not been an issue. Describe a system in which "brute force" MD struggles to achieve ergodic sampling. Describe one "enhanced sampling" technique that can be used to overcome this. [7]