Understanding advanced molecular simulation
CH-420
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General
Course Outline
- Block 0:
- Week 1: Introduction & Computational Carpentry
- Block 1:
- Week 2: Statistical Thermodynamics & Exercises 1-2
- Week 3: Statistical Thermodynamics & Exercise 3
- Week 4: Statistical Thermodynamics & Exercise 4
- Block 2
- Week 5: Monte Carlo & Exercises 1-2
- Week 6: Monte Carlo & Exercise 3
- Week 7: Molecular Dynamics & Exercises 3-4
- Week 8: Molecular Dynamics & Exercise 4
- Block 3:
- Week 9: Monte Carlo in Different Ensembles & Exercise 1
- Week 10: Molecular Dynamics in Different Ensembles & Exercise 2
- Week 11: Exercise 3
Textbook
D. Frenkel and B. Smit, Understanding Molecular Simulations: from Algorithms to Applications, 3rd ed. (Academic Press, San Diego, 2023) http://dx.doi.org/10.1016/C2009-0-63921-0.
PDF versions of some pages mentioned in exercise can be found below
- Virtual machine installation for windows system (Forum)
- Questions? (Forum)
- Presentation time slot choice (Choice)
- Some pages of "Understanding Molecular Simulation From Algorithms to Applications" 3rd version (Folder)
- Assigned Blocks (Folder)
- Oral Exam Time Schedule (Folder)
0. Exercises
- Block 1 - Statistical Thermodynamics (Folder)
- Block 2 - Monte Carlo & Molecular Dynamics (Folder)
- Block 3 - MC & MD in Other Ensembles (Folder)
1. Introduction & Computational Carpentry
In this section, we give an introduction to the computational tools that are needed to carry out the rest of the course.
- ResourcesA pdf of the introductory slides can be f... (Text and media area)
- Setup your Computational Environment (Page)
- Necessary files (Folder)
- Appendix VS code (File)
- VM_install (File)
2. Statistical Thermodynamics
In this part we review the basics of Statistical Thermodynamics
- ResourcesThe slides on Statistical Thermodynamics ... (Text and media area)
- 2.1 Introduction Statistical Thermodynamics (Text and media area)
- 2.1 Introduction (URL)
- 2.2 Molecules and Thermodynamics (Text and media area)
- 2.2.1 Thermodynamics and Molecules (URL)
- 2.2.2 Pressure and Molecules (URL)
- 2.2.3 Equilibrium and Molecules (URL)
- 2.3 Basic Statistical Thermodynamics (Text and media area)
- 2.3.1 Basic Assumption (URL)
- 2.3.2 Equilibrium (URL)
- 2.4 Different ensembles (Text and media area)
- 2.4.1 Introduction (URL)
- 2.4.2 Canonical (NVT) ensemble (URL)
- 2.4.3 Constant pressure (NPT) ensemble (URL)
- 2.4.4 Grand-canonical (μVT) ensemble (URL)
3. Monte Carlo
In this section we discuss the Monte Carlo method
- ResourcesThe slides on Monte Carlo Methods can be ... (Text and media area)
- 3.1 Introduction (Text and media area)
- 3.1 Introduction (URL)
- 3.2 Importance Sampling (Text and media area)
- 3.2 Importance Sampling (URL)
- 3.3 A simple Monte Carlo Algorithm (Text and media area)
- 3.3.1 A simple Monte Carlo Algorithm (part 1) (URL)
- 3.3.2 A simple Monte Carlo Algorithm (part 2) (URL)
- 3.3.3 A simple Monte Carlo Algorithm (part 3) (URL)
- 3.4 Unconventional Monte Carlo (Text and media area)
- 3.4.1 Non-Boltzmann sampling (URL)
- 3.4.2 Parallel Monte Carlo (URL)
4. Molecular Dynamics
In this section we discuss the basics of Molecular Dynamics
- ResourcesThe slides on Molecular Dynamics can be f... (Text and media area)
- 4.1 Introduction to Molecular Dynamics (Text and media area)
- 4.1 Introduction (URL)
- 4.2 Details of a Molecular Dynamics Algorithm (Text and media area)
- 4.2.1 Initialization (URL)
- 4.2.2.1 Calculation of the force (Part 1) (URL)
- 4.2.2.2 Calculation of the force (Part 2) (URL)
- 4.2.3 Equations of Motion (URL)
- 4.3 Liouville Formulation of Molecular Dynamics (Text and media area)
- 4.3.1 Liouville formalism (URL)
- 4.3.2 Multiple time step (URL)
- Extra: some case studies (Text and media area)
- Extra 1: Statistical Thermodynamics and Molecular Simulation: CO2 in MOF-74 (URL)
- Extra 2: Statistical Thermodynamics and Molecular Simulation: Xe/Kr separations (URL)
5. Monte Carlo in Different Ensembles
In this section we discuss how to carry out Monte Carlo in different ensembles.
- ResourcesThe slides on Monte Carlo in Different En... (Text and media area)
- 5.1 Introduction (Text and media area)
- 5.1 Introduction (URL)
- 5.2 Review of the NVT ensemble (Text and media area)
- 5.2 NVT ensemble (URL)
- 5.3 The NPT ensemble (Text and media area)
- 5.3 NPT ensemble (URL)
- 5.4 The μVT ensemble (Text and media area)
- 5.4 μVT ensemble (URL)
- 5.5 An ensemble for biological membranes (Text and media area)
- 5.5 Membranes (URL)
6. Molecular Dynamics in Different Ensembles
In the lecture on Basic Molecular Dynamics we
have shown how to carry out MD simulations in the NVE ensemble. To make
comparison with experiments easier, it is often more convenient to simulate in
the canonical (NVT) ensemble. In these lectures we discuss different methods to
carry out molecular dynamics in the NVT ensemble.
- ResourcesThe slides for Molecular Dynamics in Diff... (Text and media area)
- 6.1 Introduction (Text and media area)
- 6.1 Introduction (URL)
- 6.2 How to not NVT (Text and media area)
- 6.2 How to not-NVT (URL)
- 6.3 The Anderson Thermostat (Text and media area)
- 6.3 The Anderson Thermostat (URL)
- 6.4 Nose-Hoover thermostat Here we discuss ex... (Text and media area)
- 6.4.1 Lagrangian and Hamiltonian (URL)
- 6.4.2 Nose Hoover thermostat (URL)
Chapter 7: Free energies
In this section, we discuss the different methods to compute the free energy or the chemical potential in a molecular simulation.
- Free energiesThe slides used in the videos can be ... (Text and media area)
- 7.2 Statistical Thermo (Text and media area)
- 7.3 Methods to compute free energies (Text and media area)
- End Week 12 (Text and media area)
- 7. Hands-on (Text and media area)
- Block 4 exercise notes File (File)