Single-Course English 5 ECTS

Molecular dynamics and machine learning

Overall Course Objectives

To provide the students with a basic introduction to molecular dynamics simulations used to model molecular systems and molecular interactions. This understanding will enable them to apply, evaluate and develop simulation programs for the solution of relevant problems in chemistry, chemical engineering, physics and biology. Basic introduction to machine learning and its use in computational structural biology.

Learning Objectives

  • Explain the basic postulates and classify the different ensembles in statistical mechanics.
  • Select a stochastic variable with a given probability distribution using a uniform random number generator.
  • Explain the different steps in a molecular dynamics simulation program.
  • Explain and apply different numerical methods for integration of equations of motion.
  • Compute the time evolution of a hamonic and an anharmonic oscillator.
  • Determine the different relaxation times in the equations of motion for molecular dynamics simulations in the different ensembles.
  • Develop a molecular dynamics simulation program that can simulate a simple atomic systems.
  • Analyse simulation results and compute isothermal compressibility, pair-distribution function and time-correlation functions.
  • Explain the use of machine learning and its use in computational structural biology.

Course Content

Molecular dynamics simulation techniques (probability distributions, integration schemes, different thermodynamic ensembles, thermostats). Analysis of computer simulation results; e.g. pair distribution function, transport coefficients, time correlation functions. Working with simple machine learning tools for protein optimization. To support the learning and understanding of the theory given in the lectures, there will be hands-on exercises, where the participants will have the opportunity to modify existing programs and develop programs themselves.

Recommended prerequisites


Teaching Method

Lectures and exercises (Computer Lab)



This course forms together with physical chemistry 3 (26233) and advanced physical chemistry (26235) a natural unity, which provides the molecular basis for the thermodynamic description of equilibrium and non-equilibrium systems. The course further provides a background for studies of chemical engineering, catalysis, surface chemistry, polymer chemistry, biological chemistry, and biochemistry.

No exam in the regularly scheduled exam period

See course in the course database.





13 weeks




DTU Lyngby Campus

Course code 26255
Course type Candidate
Semester start Week 35
Semester end Week 48
Days Wed 8-12

7.500,00 DKK