Blog #2

Dr. Deng and I have been working on Amber Tutorials and test running the program “Maestro Schrodinger.” In order for me to utilize the program Maestro, I need to be proficient in all of the tutorials on Amber. Amber is a tool that teaches people how to use a molecular dynamics software. The first step was to learn the Unix Command-Line. From this tutorial I learned how to use the command line to navigate a file system, view directories view directories and copy, move, and remove files and directories. Then I did another tutorial which gave an introduction to Molecular Dynamics Simulations. This tutorial was extremely helpful because it gave me a better insight into what we are actually researching. This research is extremely beneficial to me because I get to see how the latest technology can be used in science today.


The last two weeks we actually ran into a lot of problems. Once we received the license from Maestro to use the system we were not able to register the program. Therefore, we contacted the company and are waiting for a response. We also had issues trying to connect to the server. We worked with the IT department to resolve most of the issue. Currently, I am working on 2 more tutorials. Even though Amber is a great program the site does not work that often. These obstacles have taught me that in research most of the time things do not go smoothly. We need to work together to resolve unforeseen issues and not give up. Dr. Deng and I are excited to finally be able to use Maestro. We will be continuing our research this upcoming fall semester.

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