Molecular dynamics

These pages contain the notes for the molecular dynamics course of winter 2023. The pages are updated weekly as lectures progress.

Prerequisites and installations

• Module: Installation of necessary software
• Installation of tools: WSL2/Linux etc.

Linux basics

• Linux - the basics
• Linux: Some basic & useful commands

Python and Jupyter

• Summary
• Jupyter Notebook / Jupyter Lab
• Brief introduction to Python

Molecular interactions

• Interactions
• The Lennard-Jones potential

Numerical algorithms

• Digression: A few words about finite precision
• Basic MD algorithm
• Integration of the equations of motion

Review of thermodynamics and statistical mechanics

• Review of thermodynamics
• Review of statistical mechanics
• Bibliography

Visualization

• Molecular visualization
• VMD molecular visualization software
• VMD selections
• VMD plugins

MD basics

• First look into (particle) simulations
• What is Molecular Dynamics (MD)
• Boundary conditions (BCs)

MD simulation with Gromacs

• Introduction to Gromacs
• Gromacs installation
• Simple simulation of water using Gromacs
• First look into (particle) simulations

Installation instructions

• Installation of Python and Jupyter
• Python virtual environments
• VMD installation

Extras & How-Tos

• On computation and codes
• Editing ASCII files
• The vi editor
• Helpful software