Simulating Molecular Biology: Challenges and Opportunities

This lecture delves into simulating the dynamics of molecular biology, focusing on the challenges and opportunities faced in the field. The instructor discusses the sequential nature of molecular dynamics simulations, the force fields involved, and the computational complexity of simulating interactions between atoms. The lecture covers the intricacies of Lagrange multipliers, dummy constraints, and the use of virtual interaction sites. Additionally, it explores the computational demands of simulating systems with a large number of atoms and the strategies employed to optimize performance. The presentation also touches on the hardware architecture of modern CPUs and GPUs, emphasizing the need for efficient algorithms to leverage their capabilities.