PCC-32806 Computer Modelling of Biomolecules

This Study Handbook is published with reservation. It is not official yet.


Credits 6.00

Teaching methodContact hours
Course coordinator(s)dr. RJ de Vries
Lecturer(s)prof. dr. ir. FAM Leermakers
dr. RJ de Vries
AH Westphal
prof. dr. JT Zuilhof
Examiner(s)dr. RJ de Vries

Language of instruction:


Assumed knowledge on:

Elementary mathematics; PCC-21802/23303 Introductory Thermodynamics A/B; PCC-22306 Driving Forces in Chemistry, Physics and Biology.

Continuation courses:

Thesis PCC, ORC, BIC, and more.


Computer Modelling of Biomolecules has become an indispensable tool in biomolecular science and technology, next to experiments and theory. For example, it plays a key role in the discovery of new drugs, in structure elucidation of proteins and protein complexes. Building on a basic background in physical chemistry (see assumed knowledge above), this course introduces the basic theory behind biomolecular simulation techniques such as molecular mechanics, molecular dynamics, Langevin Dynamics and Brownian Dynamics, and Monte Carlo simulations. A last part of the course deals with Quantum Chemical Modelling. While the emphasis of the course is on applications of computer simulations to biomolecules, the techniques discussed in the course apply more generally, so the course is also of interest for students that have a more general interest in computer simulations of molecules. Tutorial's with exercises are used as an aid to obtain a working understanding of the theory, and computer practicals are used to learn to work with the various simulation techniques on simple example projects.

Learning outcomes:

After successful completion of this course students are expected to be able to:
- judge relevant basic concepts in computer modelling of biomolecules: molecular forces, energy minimization, statistical thermodynamics, Schrödinger equation;
- analyse the formulas presented in the course text, lectures, and tutorials in a mathematically correct way, and apply them in simple computations (with due attention to dimensions and units);
- explain the essentials of computer modelling of biomolecules: molecular mechanics, molecular dynamics, Monte Carlo, Langevin Dynamics, Brownian Dynamics, Quantum Computations;
- properly interpret the results of computer simulations on relevant biomolecular systems.


- lectures;
- tutorials;
- computer practicals.


- written exam with open questions (70%);
- reports on computer labs (30%).
Each component needs a minimum mark of 5.5 to pass. The computers labs contribute to the final mark only if they are rated higher than the written exam. Interim results are valid for three years.


Alan Hinchliffe. (2008). Molecular Modelling for Beginners. Wiley. 428p. ISBN: 978-0-470-51314-9.

Restricted Optional for: MMLMolecular Life SciencesMScD: Spec. D Physical Chemistry6MO
MMLMolecular Life SciencesMScC: Spec. C Physical Biology6MO