Understanding Molecular Simulation

1. Introduction

Part I: Basics

2. Thermodynamics and Statistical Mechanics

3. Monte Carlo Simulations

4. Molecular Dynamics Simulations

5. Computer Experiments

Part II: Ensembles

6. Monte Carlo Simulations in Various Ensembles

7. Molecular Dynamics in Various Ensembles

Part III: Free -Energy Calculations

8. Free Energy Calculations

9. Free Energies of Solids

10. Free Energy of Chain Molecules

Part IV: Advanced Techniques

11. Long-Ranged Interactions

12. Configurational Bias Monte Carlo

13. Accelerating Monte Carlo Sampling

14. Time-Scale-separation Problems in MD

15. Rare Events

16. Mesoscopic Fluid Models

Part V: Appendices

A: Lagrangian and Hamiltonian

B: Non-Hamiltonian Dynamics

C: Non-equilibrium Thermodynamics

D: Smoothed Dissipative Particle Dynamics

E: Committor for 1-D diffusive barrier crossing

F: Linear Response Theory: examples

G: Statistical Errors

H: Integration Schemes

I: Saving CPU Time

J: Reference States

K: Statistical Mechanics of the Gibbs "Ensemble"

L: Overlapping Distribution for Polymers

M: Some General Purpose Algorithms

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• Modelagem computacional e simulação
• Física atómica e molecular
• Química física

Computational modelling; Computational chemistry; Monte Carlo simulations; Statistical mechanics; Hamiltonian; Lagranigan; Particle dynamics; Molecular dynamics; Gibbs Ensemble; Energy modelling; Materials chemistry