Topic 4 - Force fields, molecular mechanics and dynamics

In this serie of lessons, the general concepts of a force field are explained. Buidling further upon this, concept of moelcular mechanics and molecular dynamics are highlighted.

Prepare yourself:

It is highly recommended that you prepare yourselves by go through the following scientific paper and movie well in advance:

Course manual:



We will make use of a Google Colab environment to run molecular dynamics simulations of a real protein system, and a protein-ligand complex. Before running these simulations, it is required to read the following paper very carefully, because the exercises have been cloned from the GitHub repository that is the supplementary material of this paper:

The original repository with additional simulations is available on the Github repository of Pablo Arantes, the author of the original paper.

Note: you need a Google Drive account in order to run these simulations. If you don’t have this, then you need to setup one.


Then it is time to move over to the fifth and last topic of this course: