CHM 579 Assignment #2
Molecular Simulation of Simple Homogenous Systems
Due on Wednesday, Feb 15 2017 at 3:29 PM
The objective of this assignment is to learn to simulate simple systems using Monte Carlo and Molecular Dynamics. The simple systems are: Lennard-Jones fluid for Monte Carlo simulations, and Water and Carbon dioxide respectively for Molecular Dynamics.
Lennard-Jones Monte Carlo
The goal of this lab is to investigate the equation of state of Lennard-Jones fluids by using a Monte Carlo program. This is the first realistic computer simulations we run in this class. Thus, we need to learn to recognize and respect important details: periodic boundary conditions, truncation of potential, tail corrections, and the equilibration phase of the simulation.
You can read all about Monte Carlo here and we will also cover this topic in our lectures in detail.
Follow the instructions and answer questions for the program given in the PDF file for L-J fluid Monte Carlo.
You can download the zip file associated with this part of the assignment.
Molecular Dynamics with Gromacs
In this lab you will learn the basics of using the GROningen MAchine for Chemical Simulations (GROMACS) package. The two systems you will study are: Water and Carbon dioxide.
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The first system to study is liquid water by using a simple SPC/E model1. You will learn how to obtain thermodynamic observables, such as the potential energy, as well as structural and dynamic properties of the system. This is arguably the most important lab in the course. Much of the information needed to complete this lab is available in the GROMACS online manual. Refer to the manual first, before asking technical questions.
You can download the zip file associated with this part of the assignment.
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You need to follow the tutorial and test the simulation of the system of CO2 gas with 216 molecules. Then you need to answer all the questions that are asked in the tutorial of simulating argon by running the CO2 box you created in the tutorial but with the parameters mentioned in the Argon simulation tutorial. If you cannot answer any question for CO2, please specify why is the case? This will help you think about liquid and gaseous simulations.
Make a Web Page!
- Include your images/illustrations with a short explanation
- Extra Credit: It will be good to see movies of these simulations for each of the 3 parts in Assignment # 2. If you can make movies this will be taken into account. We will learn how to do this separately as well. Google search is your friend on how to make movies with simulation trajectories. Also gromacs has tutorials on how to take out the high frequency motion of the system.
- Remember, the assignments are done in publication style format only in form of webpages.
- Webpage Design Primer
- BareBones Guide to HTML
- IMPORTANT: Please do not make any plugins (Chime, etc) necessary in order to view your webpage! Use GIF/PNG/Jpeg images only, since the plugins are
not available for all browsers and might make grading difficult.
Problems? Questions about the Page or the Class?
Contact the instructor