CHM 579 Assignment #4

Molecular Dynamics of Simple Homogenous Systems

Due on Friday, 6 March 2020 at 11:59 pm

The objective of this assignment is to learn to simulate simple systems using Molecular Dynamics. 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.

Water Simulation in GROMACS

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.
The required files are located here

Molecular dynamics simulation of carbon dioxide

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.

Problems? Questions about the Page or the Class? Contact the instructor