Classical Molecular Dynamics (MD) Simulations
5. Classical Molecular Dynamics (MD) Simulations#
In this set of exercises, you will be briefly introduced to the concept of classical force fields and molecular dynamics via propagation of atomic positions in time. We will finalize our ToyMD program and run molecular dynamics of CO2 gas.
🎯 Learning goals
Review inter- and intramolecular interactions for building a classical force field
Compare common thermostat schemes
Understand how and why we initialize MD simulations
Draw a connection between the pair radial distribution function, the partition function, and ensemble average
📖 Chapter in script
Chapter 5 - Molecular Dynamics Simulations (II)
📚 Resources
Understanding Molecular Simulation, Frenkel & Smit, 2nd Edition - Chapter 6