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

You need an account in Physics to be able to join the chat. Please ask Zedat to give you an account in Physics if you don't have one already.

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