The editors of gromacs include funny quotes such as this one: “Been there, Done it” (Beavis and Butthead)
My third week in the lab consisted of working on a process called RMSD clustering. I was clustering the ankyrin trajectory files that I downloaded last week. The data came in three files, which were S04-MD-01, S04-MD-02, S04-MD-03. These are each simulations of the Ankyrin protein. For some reason I forgot about the 02, and 03 files and only clustered the first trajectory file. This small step set me back a few days, but now that I have gone through the process once, I will be able to finish it in one day.
When clustering data, all trajectory files need to be combined, or concatenated. RMSD clustering is an algorithm that groups protein configurations based on on their RMSD. I was receiving a high number of clusters after doing the RMSD Clustering on the first file, so I asked my mentor for help. She ran a few tests, and asked if I had concatenated all three files. My mentor explained why I needed to concatenate the files. Unfortunately, the week was over and I would have to concatenate all three files the following week.
My attempt at teaching myself how to surf was not going well, so I decided to take a lesson that would teach me the basics. I was able to learn the correct way to navigate through the waves, and pick the right wave to surf. Throughout the week it was helpful to get out of the lab, and catch some waves.
After my surf lesson I visited the Birch Aquarium. Even though the aquarium was small, it had many great attractions. I was able to see one of my favorite sea animals, the leafy seadragon. I have my own aquarium at home, so I was looking for an opportunity to see the filtration systems. Unfortunately the staff told me that unless I was a staff member I would not be able to, but I did catch one staff member doing maintenance under one of the tanks. I was able to ask her questions about how they run their protein skimmers as well as the UV filters.
Me with fellow Pinterns Max Cantor and Will Plantz with our host mom Lora
On Tuesday my amazing host family took me to a Padres Game. I was expecting to arrive at the stadium and have to wait in a line, but my host family had premium tickets so we were able to skip the line, and head straight to our seats where we had dinner and enjoyed the game.
The first half of my internship has been great. I am looking forward to the other half which will be filled with many more adventures!
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