Computational Molecular Physics WiSe 22/23
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 17, 2022
Last day of lectures: February 15, 2022
First tutorial: October 25, 2022
Last tutorial: February 14, 2022
Winter break: December 17, 2022 – January 1, 2023
Course Chat:
https://matrix.to/#/!wHYOaQBanpDRoygcGj:physik.fu-berlin.de?via=physik.fu-berlin.de
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Topics/Lectures:
(the schedule may be adjusted during the semester)
Oct 17 01. Introduction
Oct 19 02. Statistical Mechanics refresher
Oct 18 – No Tutorial
Oct 24 03. Statistical Mechanics refresher
Oct 26 04. From Statistical Mechanics to Molecular Dynamics
Oct 25 – Tutorial 01. Python primer
Oct 31 05. Molecular Dynamics: force-fields
Nov 2 06. Molecular Dynamics: integrators
Nov 1 – Tutorial 02. Python primer – hw 1 due
Nov 7 07. Molecular Dynamics: integrators
Nov 9 08. Molecular Dynamics: electrostatic treatment
Nov 8 – Introduction to MDtraj – hw 2 due
Nov 14 09. Molecular Dynamics: electrostatic treatment
Nov 16 10. Molecular Dynamics: electrostatic treatment
Nov 15 – Write your own integrator – hw 3 due
Nov 21 11. Molecular Dynamics: implicit & explicit solvent methods
Nov 23 12. Molecular Dynamics: simulations in different ensembles
Nov 22 – Write your own integrator – hw 4 due
Nov 28 13. Molecular Dynamics: simulations in different ensembles
Nov 30 14. Molecular Dynamics: Langevin Dynamics
Nov 29 – Use OpenMM – hw 5 due
Dec 5 15. Molecular Dynamics: Langevin Dynamics
Dec 7 16. Molecular Dynamics: equilibrium data analysis
Dec 6 – Use OpenMM – hw 6 due
Dec 12 17. Molecular Dynamics: equilibrium data analysis
Dec 14 18. Molecular Dynamics: kinetics & MSM
Dec 13 – Introduction to PyEmma – hw 7 due
Jan 2 19. Molecular Dynamics: kinetics & MSM
Jan 4 20. Molecular Dynamics: Enhanced Sampling and Adaptive Sampling
Jan 3 – Introduction to PyEmma – hw 8 due
Jan 9 21. Molecular Dynamics: Free Energy perturbation
Jan 11 22. Molecular Dynamics: coarse-graining
Jan 10 – Coarse-graining – hw 9 due
Jan 16 23. Molecular Dynamics: coarse-graining
Jan 18 24. Molecular Dynamics: machine-learning methods
Jan 17 – Normal Mode Analysis – hw 10 due
Jan 23 25. Molecular Dynamics: machine-learning methods
Jan 25 26. Finding minima and transition states in Free Energy Landscapes
Jan 24 – Monte Carlo – hw 11 due
Jan 30 27. Normal Mode Analysis
Feb 1 28. Monte Carlo simulations
Jan 31 – Summary/Preparation for exam
Feb 6 29. Markov Chain Monte Carlo
Feb 8 30. Parallel Tempering
Feb 7 – Summary/Preparation for exam
Feb 13 29. Exam week
Feb 15 30. Exam week
Feb 14 – Summary/Preparation for exam