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FCB3204 Molecular Modeling 7.5 credits

The course provides knowledge and skills in the field of molecular modeling corresponding to the third cycle.

About course offering

For course offering

Autumn 2023 Start 30 Oct 2023 programme students

Target group

Doctoral students.

Part of programme

No information inserted


P2 (7.5 hp)


30 Oct 2023
15 Jan 2024

Pace of study


Form of study

Normal Daytime

Language of instruction


Course location


Number of places

Places are not limited

Planned modular schedule


For course offering

Autumn 2023 Start 30 Oct 2023 programme students

Application code



For course offering

Autumn 2023 Start 30 Oct 2023 programme students


Mårten Ahlquist (


No information inserted

Course coordinator

No information inserted


No information inserted
Headings with content from the Course syllabus FCB3204 (Autumn 2021–) are denoted with an asterisk ( )

Content and learning outcomes

Course disposition

The course comprises approximately 200 full-time study hours and is co-read with the course BB2280. The course elements include lectures with in-depth reading and reflective analysis that form the basis for the design and implementation of an individual project where a research problem is formulated and studied (PRO1, approximately 160 full-time study hours). Computer exercises are also included (LAB1, approximately 40 full-time study hours).

The practical content of the course includes computer exercises based on the course's subject focus and an individual project related to the course's theoretical foundations. The project is based on a research question and is based on selected research articles. The project must encounter the theoretical foundations and the skills acquired in the computer exercises with the student’s research topic leading to an original work in the form of a written report. The theoretical basis for the research question must be obtained and a project plan must be prepared before the design and implementation phase begins

Course contents

The course's theoretical content includes:

  • Introduction to quantum chemistry: Molecular orbital theory, semi-empirical methods
  • Basic density functional theory (DFT)
  • Molecular mechanics and molecular dynamics
  • Monte Carlo methods
  • Energy minimization and potential energy surfaces
  • QM/MM methods
  • Solvation and surrounding effects
  • Theoretical methods in drug discovery: Docking, protein structure prediction, QSAR
  • Simulation of chemical reactions in solution
  • Modeling of enzymatic catalysis

Intended learning outcomes

After completion of the course the student shall be able to

  • demonstrate in-depth knowledge and analytical ability in molecular modeling adequate for the level of educational level of the course, and critically review others' work in the field [LAB1, PRO1]
  • demonstrate good ability to explain and analyze complex concepts in molecular modeling based on relevant research literature, and in a pedagogical way communicate the knowledge in writing and orally [PRO1]
  • be able to reflect on and describe how scientific issues in the field's research can contribute to sustainable societal development [PRO1]

Literature and preparations

Specific prerequisites

Eligible for studies at the third-cycle level.

Recommended prerequisites

BB2280, or equivalent knowledge from another course.


No information inserted


Announced at course start.

Examination and completion

If the course is discontinued, students may request to be examined during the following two academic years.

Grading scale

P, F


  • LAB1 - Laboratory work, 1.5 credits, grading scale: P, F
  • PRO1 - Project, 6.0 credits, grading scale: P, F

Based on recommendation from KTH’s coordinator for disabilities, the examiner will decide how to adapt an examination for students with documented disability.

The examiner may apply another examination format when re-examining individual students.

Grading criteria are specified in the course PM.

Other requirements for final grade

Required for final grade: 90% attendance at lectures, written critical reflection for selected scientific articles, approved written project report and completed oral project presentation (PRO1); and attendance on computer exercises and completed exercise reports (LAB1).

Opportunity to complete the requirements via supplementary examination

No information inserted

Opportunity to raise an approved grade via renewed examination

No information inserted


Ethical approach

  • All members of a group are responsible for the group's work.
  • In any assessment, every student shall honestly disclose any help received and sources used.
  • In an oral assessment, every student shall be able to present and answer questions about the entire assignment and solution.

Further information

Course room in Canvas

Registered students find further information about the implementation of the course in the course room in Canvas. A link to the course room can be found under the tab Studies in the Personal menu at the start of the course.

Offered by

Main field of study

This course does not belong to any Main field of study.

Education cycle

Third cycle

Add-on studies

No information inserted


Mårten Ahlquist (

Transitional regulations

If the course is discontinued, the student is given the opportunity to be examined on the course for another two academic years.

Postgraduate course

Postgraduate courses at CBH/Theoretical Chemistry and Biology