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Lecture 14
Molecular system representations

Date: Oct 22, 2024

Building on the foundations from the previous lecture, this session focuses on the practical aspects of setting up and running MD simulations. We'll walk through the steps involved in preparing a system for simulation.

Note

I decided to go over MD relaxations a second time for L15 and moved those slides there.

Learning objectives

What you should be able to do after today's lecture:

  1. Explain why DHFR is a promising drug target.
  2. Select and prepare a protein structure for molecular simulations.
  3. Explain the importance of approximating molecular environments.
  4. Describe periodic boundary conditions and their role in MD simulations.
  5. Explain the role of force field selection and topology generation.
  6. Outline the process of energy minimization and its significance.

Readings

Relevant content for today's lecture if you are interested.

Presentation