Class 02: Setup a MD simulation system using GROMACS software package

27 Novembro 2020, 09:30 • Miguel Machuqueiro

In this class, we develop a system setup focused on the chosen protein using common bash scripts to call the GROMACS software package.  Please note that in this tutorial the students will not be performing the simulations per se since these are very time-consuming. However, they can check out the input files and investigate the complete workflow: system building, energy minimization, initialization of temperature and pressure, and finally, they will perform some common trajectory analyses.