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Lecture 13
Molecular simulation principles

Date: Oct 17, 2024

This lecture introduces the fundamental principles of molecular dynamics (MD) simulations. We'll explore the theoretical foundations of MD, including force fields and integration algorithms. The session will cover the basic concepts needed to understand how MD simulations provide a dynamic view of molecular systems, complementing static structural data.

Learning objectives

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

  1. Understand the importance of molecular dynamics (MD) simulations for proteins.
  2. Identify the validity of the classical approximation.
  3. Discuss the concept of equations of motion in MD simulations.
  4. Explain the role of integration algorithms in MD simulations.
  5. Describe the components of a molecular mechanics force field.
  6. Understand noncovalent contributions to force fields.
  7. Identify data for force field parameterization

Readings

Relevant content for today's lecture.

  • None! Just the slides (and Google).

Presentation