Molecular Modelling
Contents (Beschrijving)
The topic of this course is the different aspects of molecular modelling. The concepts behind different modelling software packages will be discussed. The focus will be to on classical methods. The following topics will be treated:  Monte Carlo methods
 Molecular Dynamics
 Optimization methods
 Free Energy Determination
 Transition state location methods

Objectives (Leerdoelen)
The student should be able to
 understand the basic concepts behind the molecular dynamics, (kinetic) Monte Carlo, Free Energy Determination and Transition state location methods
 make a motivated choice between the different modelling techniques
 make simple code for optimization and Metropolis and kinetic Monte Carlo

Examination (Tentaminering)
Three hour written exam (mark) and computer assignments that should be completed satisfactory.

Recommended reading (Aanbevolen literatuur)
Lecture notes will be made available online. For background reading I refer to:

Weekly targets
 Week 1: Chapters 1, 2 and 3 (until 3.2.1)
 Week 2: Chapters 3 and 4
 Week 3: Chapters 5, 6 and 7
 Week 4: Chapter 8
 Week 5: Chapter 9
 Week 6: Chapter 10
 Week 7: Chapter 11
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Lectures notes
Lecture notes
Recommended reading (Aanbevolen literatuur)
Computer Exercises
Make sure that you have access to MATLAB or OCTAVE or something similar.
A MATLAB tutorial and
a MATLAB Cheat Sheet can be useful as well.
The commented codes of Exercises 7 and 11 should be handed in. Deadline: end of final computer tutorial in week 7.
Week 1
Week 2
Week 3 The commented code of Exercise 7 should be handed in through Brightspace.
Week 4
Week 5
Week 6