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: For Metropolis Monte Carlo and Molecular Dynamics: Understanding Molecular Simulation: From Algorithms to Applications (Daan Frenkel and Berend Smit) (2nd edition) For kinetic Monte Carlo: Introduction to the Kinetic Monte Carlo Method (A.F. Voter)

Weekly targets Week 1: Chapters 1, 2 and 3 (until 3.2.1) Week 2: Chapters 3 and 4 Week 3: Chapters 5 and 6

Setting up your environment

Linux

• We will use several programs which are available under linux. GMOLDEN for visualisation and some modelling, MATLAB for writing a few algorithms and some other smaller programs as well.
• You will need to set up the computer such that you can run all these programs.
• Login using your favoured session type. Mine is "KDE" but "Gnome" is fine as well.
• Start a terminal. The following commands are good to remember:

                  	    ls    "view a list of files in a directory"
                  	    mkdir "make a directory"
                  	    cd    "change to directory"
                  	    pwd   "give current directory"
                  	    cp    "copy a file"
                  	    mv    "move or rename a file"
                  	    rm    "remove a file"
                  	    less  "view a file"
                  	    

• Make sure that you work in the bash-shell by typing

                  	    echo $0
                  	    

  If this does not list bash, type bash. Then give the following set of instructions

                  	    cd ~
                  	    mkdir MM
                  	    cd MM
                  	    cp /vol/cursus/MolecularModeling/setup/.setup .
                  	    source ~/MM/.setup
                   	    

• Each time before you start, you will need to check your shell (bash) and type source ~/MM/.setup

Lectures notes

Lecture notes
Recommended reading (Aanbevolen literatuur)

• Paper on pitfalls of Molecular Simulations Simulations: the dark side (Daan Frenkel)
• Molecular Modelling for Beginners (A. Hinchliffe) Chapters 1-10 (2nd edition)
• For Metropolis Monte Carlo and Molecular Dynamics: Understanding Molecular Simulation: From Algorithms to Applications (Daan Frenkel and Berend Smit) (2nd edition)
• For kinetic Monte Carlo: Introduction to the Kinetic Monte Carlo Method (A.F. Voter)

Exercises

Werkcollege 1
The paper needed for exercise 2
Solution 1
Werkcollege 2: Genetic algorithm and Verlet integrator
Werkcollege 3: Kinetic Monte Carlo of H on graphite
Solution 3
Werkcollege 4: Properties and HTST

Computer Exercises

Make sure you have your linux environment correctly set-up (Getting Started).
All files that contain molecular structures can be obtained from /vol/cursus/MolecularModeling/molecules.

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 8.

Exercise 1: Setting up your environment, Exercise 2: Obtaining structures from databases, Exercise 3: Examine a 2D Potential Energy Surface, and Exercise 4: Calculation of point charges
Exercise 5: Calculation of the energy and geometry optimization for naphthalene and Exercise 6: Implementing a Minimizer in a Computer Program
Exercise 7: Nudged Elastic Band The commented code of this exercise should be handed in
Exercise 8: Molecular Dynamics
Exercise 9: Metropolis Monte Carlo
Exercise 10: The n-fold way
Exercise 11: Kinetic Monte Carlo The commented code of this exercise should be handed in