S-114.260 L Molecular Modeling

4-6 cr. (in Finnish: 4-6 opintoviikkoa)

Instructors: Mikko Karttunen (course coordinator), Laboratory of Computational Engineering, Helsinki University of Technology and Ilpo Vattulainen, Laboratory of Physics, Helsinki University of Technology

Email: mikko.karttunen@hut.fi
Tel: 451 4842
Location: Lecture room B317 (Innopoli 2, Tekniikantie 14)
Time: Spring 2005 or fall 2005 depending on the number of students. Please email the lecturer if you are planning to attend this course.

Language of instruction: English
Prerequisites: Basic statistical physics and thermodynamics, knowledge of a programming language, preferrably C or Fortran77/90. S-114.250 Special topics in computational science or a working knowledge of basic molecular dynamics & Monte Carlo methods
Course material: A.R. Leach: Molecular modeling & lecture notes. Here is the contents of the course book:
  1. Useful Concepts in Molecular Modelling.
  2. An Introduction to Computational Quantum Mechanics.
  3. Advanced AB Initio Methods, Density Functional Theory and Solid-State Quantum Mechanics.
  4. Force Field Models: Molecular Mechanics.
  5. Energy Minimisation and Related Methods for Exploring the Energy Surface.
  6. Computer Simulation Methods.
  7. Molecular Dynamics Simulation Methods.
  8. Monte Carlo Simulation Methods.
  9. Conformational Analysis.
  10. Protein Structure Prediction, Sequence Analysis and Protein Folding.
  11. Four Challenges in Molecular Modelling: Free Energies, Solvation, Reactions and Solid-State Defects.
  12. The Use of Molecular Modelling and Chemoinformatics to Discover and Design New Molecules.


  13. Review of commonly used molecular modeling software, e.g. Gromacs and NAMD

Additional reading/references: Understanding Molecular Simulation: From Algorithms to Applications D. Frenkel and B. Smit, Academic Press (1996), M. Allen and D. Tildesley, Computer Simulation of Liquids, Oxford University Press (1989), D. Rapaport, The Art of Molecular Dynamics Simulation (Cambridge), D.J. Rapaport, The Art of Molecular Simulation, D.W. Heermann, Computer Simulation in Theoretical Physics.

Assessment: Homework problems, project work & possibly an exam (this will be decided when the course begins) .