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What is Molecular Dynamics (MD)?

Molecular dynamics is a computer simulation technique where the time evolution of a set of interacting atoms is followed by integrating their equations of motion.

Simply put, MD simulations help us model complex molecular systems computationally. We shall cover more details in the upcoming chapters.

The outline of the blog roughly follows the following structure:

  • Why we do MD simulations
  • Dumbing the system down to make complex concepts simpler.
  • Explaining statistical mechanics concepts
  • Performing molecular simulations on simple systems.
  • Slowly increasing the number of degrees of freedom.
  • Looking into biased methods of simulation.
  • Understanding how to extend the concepts we learnt with simpler systems to complex systems.