Lecture 10B
Atomistic insight

Methodology

Date: Mar 20, 2025

DRAFT

This page is a work in progress and is subject to change at any moment.

This final lecture in the MD series focuses on the analysis and interpretation of MD simulation data. We'll explore common analysis techniques and how to extract meaningful biological insights from simulation trajectories.

Learning objectives

After today, you should better understand:

1. Molecular ensembles and their relevance.
2. Maintaining thermodynamic equilibrium.
3. Relaxation and production MD simulations.
4. RMSD and RMSF as conformational changes and flexibility metrics.
5. Relationship between probability and energy in simulations.

Supplementary material

Relevant content for today's lecture.

• Any scientific literature.

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

1. Drug development pipeline.
2. Role of structure-based drug design.
3. Thermodynamics of binding.
4. Enthalpic contributions to binding.
5. Entropic contributions to binding
6. Alchemical free energy simulations