1. Molecular Mechanics
Molecular Dynamics

2. Control questions
Write and solve the Newton equation of motion for a one-dimensional harmonic oscillator.
Write an expression of energy of a water molecule suitable for molecular dynamics. Explain the symbols/terms.
What is the difference the Monte Carlo method and molecular dynamics; what do they have in common?
What is the difference between molecular dynamics and molecular mechanics?
What are the restrictions of molecular dynamics, in comparison to quantum dynamics? What are the advantages of MD?

3. linux operation system Tinker molecular dynamics
Independent work
linux operation system
Tinker molecular dynamics
example computations
- PBS, NVT/NpT ensembles