Molecular Dynamics

This tutorial aims to equip you with the knowledge about molecular dynamics and answer the following questions: (1) what molecular dynamics is, (2) why we run molecular dynamics, (3) how molecular dynamics works and (4) how to run a real molecular dynamics process.

Contents:

• Before you start
• What is Molecular Dynamics?
  • Experiments on a computer
  • Why do we run MD?
  • The inputs and outputs of MD
• Starting with a simple example
  • Basic knowledge
  • The construction of theoretical models - generating force fields
  • Preparation for simulation
  • Simulation
  • Results
• An advanced example
  • Building Model
  • Solvent
• Rare Events and Enhanced Sampling
• AI in MD
• References