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Atomistic Scale Simulations
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1. Introduction
1.1. Why are we interested in the atomistic scale?
1.2. What are Simulations?
2. Molecular Models and Interactions
2.1. Introduction
2.2. Molecular Models
2.3. Periodic Boundary Conditions
2.4. Intermolecular Potentials
2.5. Short-Ranged Intramolecular Potentials
2.6. Long-Range Potentials
3. Statistical Mechanics and Thermodynamics
3.1. Introduction
3.2. Thermodyanmics and Ensembles
3.3. Statistical Mechanics: Ensembles, Ergodicity, and Other Stuff
3.4. Thermodyanmics Properties
3.5. Entropy and Temperature
3.6. Structural Correlations
3.7. Transport Coefficients
3.8. Statistical Errors
4. Molecular Dynamics
4.1. Introduction
4.2. Verlet Integration
4.3. Thermostats
4.4. Langevin Dynamics
4.5. Using MD Packages
4.6. Initialization and Neighbor Searching
4.7. HPC (High-Performance Computing)
5. Monte Carlo Simulations
5.1. Introduction
5.2. Random Numbers
5.3. Monte Carlo Methods
5.4. Sampling Methods
5.5. Gibbs Ensemble and Phase Coexistence
5.6. Phase Transitions, Finite-Size Scaling and Renormalization Group
5.7. Variance Reduction Techniques
5.8. Metropolis Method
5.9. The Ising Model
5.10. Directed Monte Carlo
5.11. Kinetic Monte Carlo
5.12. Free Energy Estimation in Simulations
6. References
7. Credits
Repository
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Index