Hello everyone and welcome back to my blog! This week I will be discussing what I did during my last week working with Igor Vorobyov, before we move onto to our final week of the internship. We started off the week by continuing to figure out QuickMD, a software that could show us the function of an ion channel over time. Despite our troubles with it last week, we were able to get it running on most of our computers. This provided us with small video of the model and many graphs depicting all the information collected. We had a long discussion where we learned what this all meant. Then we were tasked with trying to count the number of ions that passed through the channel. I reviewed the simulation we created frame by frame to get the result, 7 ions. Then we were able to calculate even more information about the ion channel through solving equations with the numbers we got. Attached below is one of the graphs we came up with in the process of running our simulation.
Later on in the week, we got to listen to another one of Igor’s lectures he gives to his students. This one was on the many different sampling methods used in Computer Aided Drug Discovery. The common issue ran into while sampling is that you need the system to reach every state but it will often get stuck in the energy minima. Igor showed us a graph that depicts the changes in energy to help us understand the concept. Then we learned about the different methods used to solve this problem. The ones that caught my interest the most were umbrella sampling, where run multiple small simulations, rather than one large one, to cover the entire system, and free energy perturbations, where you manipulate the energy levels to complete the simulation. After watching his presentation we discused how these methods were useful in Molecular Dynamics.
To finish off the week, we played around with QuickMD some more and discussed any questions we had about what we had learned so far. I am so thankful to Igor for the hands on experience he has given me the past two weeks and can’t wait to see what the last week of this experience will bring! Thanks for reading and see you next week!
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