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A Primer on Molecular Dynamics
7.8k words, 36 minutes reading time
Over very many hours of compute time, we’ll end up a massive stack of data known as a trajectory, which will encode the position and velocities for every particle in our system from timestep-to-timestep, showing the molecular dance that occurs. Because MD time-steps are limited to femtoseconds — due to increasing instability and inaccuracy upon integrating Newton’s second law if pushed beyond that — a huge tail of biological phenomena are extremely difficult to model reasonably well. Unlike how we treated force fields and simulation, I am going to stay away far away from the math on this one — I have talked about quantum stuff enough times with physicist friends to understand that attempting short-form explanation of it is rarely worth it.
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