Please note ...

IMPORTANT! - The exam for the course "introduction to biomolecular simulations" will be on the last week of September. It will be split in a written and an oral parts as follows.

Written part: Tuesday 26.09.2017, 10h-13h, room 01.402
There will be some problems and conceptual questions that you will have to explain in a concise and clear way.

Oral part: Thursday 28.09.2017, 10h-18h, room 01.402
We will give you the chance to defend or explain your answers in the written part. We will also ask some practical questions not covered in the written part.

The oral part will be closed doors and we estimate that it will take ca. 20-30 minutes per person.
Books, notes, cellphones, etc. will not be allowed in neither the written or the oral exam. You can bring a calculator.

Notice that the aula is 01.402, i.e. 1st floor above our usual seminar room 401!

Introduction to Biomolecular Simulations

Please Note: The Lecture List and topic summary of the first part of the course is now available under "Course Documentation"
Montags 10:00 - 12:00 Uhr, ab 08. Mai 2017
Institut für Biophysik,
Max-von-Laue-Str. 1, Goethe-Uni Frankfurt
Dozenten: Dr. Albert Ardèvol - Dr. Roberto Covino

Die Vorlesungen sind für 2 Wochenstunden geplant, die Übungen für 4 Wochenstunden im zweiwöchigen Rhythmus (2V + 2Ü = 4 SWS); die Termine für die Übungen werden noch bekannt gegeben.

Weitere Informationen werden durch Aushang am Institut für Biophysik bekannt gemacht.

Bei Rückfragen wenden Sie sich bitte an die Dozenten:
Dr. Albert Ardèvol (albert.ardevol(at) bzw.
Dr. Roberto Covino (roberto.covino(at)
oder das Sekretariat des Instituts für Biophysik,
Frau Rieger (069/798-46410).

First part

  • Review of probability theory.
  • Primer in equilibrium statistical mechanics, with review of the necessary classical mechanics and mathematics. Highlights on biomolecules.
  • Introduction to stochastic phenomena. Gaussian noise, Brownian motion, diffusion (Fokker-Planck equation).
  • Two state systems.
  • Kramer’s theory for thermally activated processes. Protein folding.
  • Numerical simulations. Euler algorithm for Brownian motion.

Second part

  • Molecular dynamics simulations
  • Introduction on MD + equilibrium MD.
  • Molecular dynamics. Scales in time and space. Atomistic and coarse-grained MD.
  • Biophysical Interactions, all-atom Force fields and coarse grain force field (Martini).
  • Production code and parallel computing. Introduction to GROMACS
  • Predicting biophysical properties.
  • Periodic boundary conditions. Ewald’s summation for electrostatics.
  • Thermostats & Barostats.


Max-Planck-Institut für Biophysik

Introduction to Biomolecular Simulations Course
Dr. Albert Ardèvol
Dr. Roberto Covino
Abteilung Theoretische Biophysik

Tel.: +49 (0) 69 6303-2509
E-Mail: albert.ardevol(at)
E-Mail: roberto.covino(at)

Abteilung Theoretische Biophysik:

Teaching Activities

Marie Skłodowska-Curie - Fellowship

Course announcement