Understanding Molecular Simulation

Daan Frenkel is based at the FOM Institute for Atomic and Molecular Physics and at the Department of Chemistry, University of Amsterdam. His research has three central themes: prediction of phase behavior of complex liquids, modeling the (hydro) dynamics of colloids and microporous structures, and predicting the rate of activated processes. He was awarded the prestigious Spinoza Prize from the Dutch Research Council in 2000. Berend Smit is Professor at the Department of Chemical Engineering of the Faculty of Science, University of Amsterdam. His research focuses on novel Monte Carlo simulations. Smit applies this technique to problems that are of technological importance, particularly those of interest in chemical engineering.

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