Molecular Dynamics and Monte Carlo
Molecular Dynamics and Monte Carlo
Information
1. Grading and attendance
2. Contents
3. Computer environment
4. Questions
5. References
Exercises
1. Basic Concepts of Molecular Dynamics and Monte Carlo Simulations
1.1. From Quantum to Classical Mechanics: The Example of Forces
1.2. Statistical Approaches to Numerical Estimation
1.3. Exercises
1.4. Appendix: Monte Carlo Pi Python
1.5. Appendix: Monte Carlo C++ Program
1.6. Appendix: Random and Pseudo-random Numbers
2. Statistical Thermodynamics and the Boltzmann Distribution
2.1. Statistical Thermodynamics and the Boltzmann Distribution
2.2. Reduced units
2.3. Theory Questions
2.4. Practical Questions
2.5. Appendix: Python code
2.6. Comparison linear rotor approximate versus analytical Z
2.7. Appendix: C++ code
3. Monte Carlo Simulations and the Photon Gas
3.1. Theory
3.2. Exercises
3.3. Practical: Photon gas
3.4. Appendix: Photon C++ Program
3.5. Appendix: Configurational sampling python program
4. Introduction to Molecular Dynamics
4.1. Theory
4.2. How to run the exercises
4.3. Questions
5. Classical Molecular Dynamics (MD) Simulations
5.1. Theory
5.2. How to run the exercises
5.3. Exercises
6. Properties from Molecular Dynamics
6.1. Theory
6.2. Protein Modelling
6.3. Practical: TRP Cage using OpenMM
6.4. Hbond moving average and RMSD
6.5. Exercises
Index