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Preparing and Carrying out an Molecular Dynamics (MD) Simulation

Proteins are essential to living organisms and can act as enzymes that speed up biological reactions. With molecular dynamics (MD) and other computational visual tools like NAMD, PyMOL and VMD, we can gain a closer look than a wet lab could. The multiple uses of MD include carrying experiments out in a cheaper manner, examining ligand interactions, molecular movements on an atomic level, and looking at the result of replacing amino acids. In my project, I learned about MD simulations, and also the 3-D visual aid programs.To do an MD simulation, you must first go through a series of steps with VMD and NAMD to set a molecule up. This also involved learning about Linux commands, as coding on the Linux command line is vital to the entire process. There are a series of detailed videos from the Theoretical and Computational Biophysics Group (at University of Illinois at Urbana) Champaign ( that I went through in order to understand the inner workings of each of the programs. This gave me the ability to learn more about proteins including, but not limited to, ubiquitin and DHFR. Linux is a fairly new operating system to Westfield State University, which my entire project took advantage of and allowed me to carry out solvating the proteins, minimizing, preparing, and many other functions. Overall, my goal was to be well-versed in the preparation of a protein for an MD simulation, and possibly even carry one out.

Olivia Murphy '23
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