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) no longer than 1500 words. The report should be structured:
- Abstract
- Introduction
- Aims and Objectives
- Methods
- Results and Discussion
- Conclusion
- References
Relevant supplementary material can be added at the end of the report so long as it supports your discussion. The marking criteria can be found in the Scheme for the Award of Honours (just like your bachelors and masters projects will be!) but importantly, work that presents an engaging dialogue and valid conclusion based on legitimate evidence will score highly. Presentation of results is arguably the most crucial part of science; you don't just show anything to the scientific community (for fear of inaccuracies being broadly spread and a retraction asked of you!), you show something relevant and defensible.
The abstract is often confused with a conclusion because we're not really taught how to write one. It's a section you write at the end and doesn't go into as much detail as the conclusion but you sum up the relevance of the research (intro), what you have done, what results do you have to show that you have done this and the ultimate conclusion.
Your introduction paints a picture of the background of the research; what has been done by others and where is the niche for your work. How will your work benefit the community - maybe it's a new technique. You open up the niche so the subsequent discussion inserts your work into the existing community or (for high impact journals like Nature) creates a question and novel direction that can be picked up and worked on by other interested parties. In this lab, it would be good if you can demonstrate some of the importance of your results and impact it had on Science and society.
Reproducibility of data reinforces the high standards and quality expected for a piece of work in a peer reviewed journal. It also engenders the work with legitimacy. Your Methods section, just like in synthesis, should be short and sweet. Just like "5ml of DMSO was added", in computational you say "the tip4p/2005 forcefield was used". Unlike Synthesis, you are encouraged to explain your choice for each of the methods (a little more verbose than Synthesis!).
Results and Discussion is exactly what it says on the tin - most of you will be good at writing this section! Present a result using a method described and discuss what this result means and how your results show it.
Conclusions - tie up the research and what your results show. Reread your intro, what are you trying to do? How does your research do this?
This lab, not only should provide an interesting computational invetigation, but also we want to help you start to get into the practice of proper scientific writing before your projects this or next year. The lab itself to start with is pretty self-explanatory. Work through the exercises and think about what each of your result mean physically. We ask you to perform an individual investigation at the end - there isn't really a wrong answer! - try to think about your own experiment before asking others what they did. If you present something interesting in an engaging way, you will score highly. If anything is not clear here, please ask me in the lab or by email. Reports should be submitted to Blackboard by the end of the week.
Getting Help
The demonstrators and assessors for this exercise are Ollie Robotham (oliver.robotham12@imperial.ac.uk) and Ollie Gittus (org12@ic.ac.uk). Either one of us will be available in the second floor chemistry computer room between 2pm and 3pm on each day of the experiment. If you have questions outside of these times, you are of course welcome to send them by e-mail.
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.
