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Molecular Dynamics and Monte Carlo
Molecular Dynamics and Monte Carlo
Exercises
1. Basic Concepts of Molecular Dynamics and Monte Carlo Simulations
1.1. From Quantum to Classical Mechanics: The Example of Forces
1.3. Monte Carlo
\(\pi\)
1.4. Appendix: Random and Pseudo-random Numbers
2. Statistical Thermodynamics and the Boltzmann Distribution
2.1. Statistical Thermodynamics and the Boltzmann Distribution
2.2. Boltzmann Distribution Harmonic Oscillator
3. Monte Carlo Simulations and the Photon Gas
3.1. Theory
3.2. The Photon Gas
3.3. The Lennard-Jones Potential
4. Introduction to Molecular Dynamics
4.1. Theory
4.2. MD simulation from scratch
5. Classical Molecular Dynamics (MD) Simulations
5.1. Theory
5.2. ToyMD
6. Properties from Molecular Dynamics
6.1. Theory
6.2. Protein Modelling
6.3. Practical: TRP Cage using OpenMM
6.4. TrpCage Analysis
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Index