Our research group has done a few AMBER tutorials during the Fall 2018 semester, and we will meet twice a week during winter break to continue the research. These tutorials provided us information about how to use the AMBER software and how to run simulations efficiently. Tutorial B1 is one of them and it prepares our research group well for the future steps.
The goal of AMBER tutorial B1 is to simulate a DNA polyA-polyT Decamer. First we made sure that the required files prmtop, rst7, mdin are set up. Then we performed basic RMSd analysis and visualized the results with VMD. After that we used the Born implicit solvent model to run MD simulation for the DNA model. Last we used TIP3P explicit water to run production simulation.