
S114.260 L Molecular Modeling
46 cr. (in Finnish: 46 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. S114.250 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:
 Useful Concepts in Molecular Modelling.
 An Introduction to Computational Quantum Mechanics.
 Advanced AB Initio Methods, Density Functional Theory and SolidState Quantum Mechanics.
 Force Field Models: Molecular Mechanics.
 Energy Minimisation and Related Methods for Exploring the Energy Surface.
 Computer Simulation Methods.
 Molecular Dynamics Simulation Methods.
 Monte Carlo Simulation Methods.
 Conformational Analysis.
 Protein Structure Prediction, Sequence Analysis and Protein Folding.
 Four Challenges in Molecular Modelling: Free Energies, Solvation, Reactions and SolidState Defects.
 The Use of Molecular Modelling and Chemoinformatics to Discover and Design New Molecules.
AND
 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) .

