Justin A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
University of Maryland, Baltimore
This example will guide a new user through the process of building a linear molecule using virtual sites. The tutorial assumes the user is familiar with basic GROMACS workflows and topology organization.
This tutorial assumes you are using GROMACS version 5.0 or newer. Older (pre-4.5) versions of GROMACS will not work with the example shown here due to changes to the topology format and nomenclature.
You need to follow this 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 this 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.
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.
Any problems? Please contact the instructor by email.