Computational Molecular Physics WiSe 23/24
Description
This course discusses modern methods for simulations of molecular systems, with examples and applications.
Requirements:
- Basic knowledge of statistical mechanics
- Basic programming in Python or related
The first part of the course is also offered within the module „Molecular Simulation I“ of the Master’s program in Computational Sciences.
32 lectures (30 + exam week)
Monday 12-14 0.1.01 Hörsaal B - Arnimallee 14
Wednesday 12-14 0.1.01 Hörsaal B - Arnimallee 14
Tutorials: Tuesday 10-12 1.3.01 PC-Pool - Arnimallee 14
First day of lectures: October 16, 2022
Last day of lectures: February 14, 2022
First tutorial: October 24, 2022
Last tutorial: February 13, 2022
Winter break: December 21, 2022 – January 7, 2023
Course Chat:
https://matrix.to/#/!wGiJSosGXJpOyFQhhL:physik.fu-berlin.de?via=physik.fu-berlin.de
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Topics/Lectures:
(the schedule may be adjusted during the semester)
Oct 16 01. Introduction
Oct 18 02. Statistical Mechanics refresher
Oct 17 – No Tutorial
Oct 23 03. Molecular Dynamics: force-fields
Oct 25 04. Molecular Dynamics: integrators
Oct 24 – Tutorial 01. Python primer
Oct 30 05. Molecular Dynamics: integrators
Nov 1 06. Molecular Dynamics: electrostatic treatment
Oct 31 – Tutorial 02. Python primer – hw 1 due
Nov 6 07. Molecular Dynamics: electrostatic treatment
Nov 8 08. Molecular Dynamics: electrostatic treatment
Nov 7 – Tutorial 03. Introduction to MDtraj – hw 2 due
Nov 13 09. Molecular Dynamics: implicit & explicit solvent methods
Nov 15 10. Molecular Dynamics: simulations in different ensembles
Nov 14 – Tutorial 04. Write your own integrator – hw 3 due
Nov 20 11. Molecular Dynamics: simulations in different ensembles
Nov 22 12. Molecular Dynamics: Langevin Dynamics
Nov 21 – Tutorial 05. Write your own integrator – hw 4 due
Nov 27 13. Molecular Dynamics: Langevin Dynamics
Nov 29 14. Molecular Dynamics: equilibrium data analysis
Nov 28 – Tutorial 06. Use OpenMM – hw 5 due
Dec 4 15. Molecular Dynamics: equilibrium data analysis
Dec 6 16. Molecular Dynamics: kinetics & MSM
Dec 5 – Tutorial 07. Use OpenMM – hw 6 due
Dec 11 17. Molecular Dynamics: kinetics & MSM
Dec 13 18. Molecular Dynamics: Enhanced Sampling and Adaptive Sampling
Dec 12 – Tutorial 08. Introduction to PyEmma – hw 7 due
Dec 18 19. Molecular Dynamics: Free Energy perturbation
Dec 20 20. Molecular Dynamics: coarse-graining
Dec 17 – Tutorial 09. Introduction to PyEmma – hw 8 due
Jan 8 21. Molecular Dynamics: coarse-graining
Jan 10 22. Molecular Dynamics: machine-learning methods
Jan 9 – Tutorial 10. Coarse-graining – hw 9 due
Jan 15 23. Normal Mode Analysis
Jan 17 24. Finding minima and transition states in Free Energy Landscapes
Jan 16 – Tutorial 11. Normal Mode Analysis – hw 10 due
Jan 22 25. Monte Carlo simulations
Jan 24 26. Markov Chain Monte Carlo
Jan 23 – Tutorial 12. Monte Carlo – hw 11 due
Jan 29 27. Parallel Tempering
Jan 31 28. Work on the final project
Jan 30 – Tutorial 13. Summary/Preparation for the exam
Feb 5 29. Work on the final project
Feb 7 30. Work on the final project
Feb 6 – Tutorial 14. Summary/Preparation for the exam
Feb 12 29. Work on the final project
Feb 14 30. Work on the final project
Feb 13 – Tutorial 15. Summary/Preparation for the exam