529-0004-01L  Classical Simulation of (Bio)Molecular Systems

SemesterAutumn Semester 2022
LecturersP. H. Hünenberger, J. Dolenc, S. Riniker
Periodicityyearly recurring course
Language of instructionEnglish



Courses

NumberTitleHoursLecturers
529-0004-01 GClassical Simulation of (Bio)Molecular Systems
2 hr lecture + 2 hr exercise session in the computer room
Either on Tuesdays 7:30-9:30 a.m. or on Thursdays 7:45-9:45 a.m.
The course was previously named CSCBP.
4 hrs
Tue09:45-11:30HCI D 2 »
P. H. Hünenberger, J. Dolenc, S. Riniker

Catalogue data

AbstractMolecular models, classical force fields, configuration sampling, molecular dynamics simulation, boundary conditions, electrostatic interactions, analysis of trajectories, free-energy calculations, structure refinement, applications in chemistry and biology. Exercises: hands-on computer exercises for learning progressively how to perform an analyze classical simulations (using the package GROMOS).
ObjectiveIntroduction to classical (atomistic) computer simulation of (bio)molecular systems, development of skills to carry out and interpret these simulations.
ContentMolecular models, classical force fields, configuration sampling, molecular dynamics simulation, boundary conditions, electrostatic interactions, analysis of trajectories, free-energy calculations, structure refinement, applications in chemistry and biology. Exercises: hands-on computer exercises for learning progressively how to perform an analyze classical simulations (using the package GROMOS).
Lecture notesThe powerpoint slides of the lectures will be made available weekly on the website in pdf format (on the day preceding each lecture).
LiteratureSee: Link
Prerequisites / NoticeSince the exercises on the computer do convey and test essentially different skills than those being conveyed during the lectures and tested at the oral exam, the results of the exercises are taken into account when evaluating the results of the exam (learning component, possible bonus of up to 0.25 points on the exam mark).

For more information about the lecture: Link

Performance assessment

Performance assessment information (valid until the course unit is held again)
Performance assessment as a semester course
ECTS credits6 credits
ExaminersP. H. Hünenberger, J. Dolenc, S. Riniker
Typesession examination
Language of examinationEnglish
RepetitionThe performance assessment is offered every session. Repetition possible without re-enrolling for the course unit.
Mode of examinationoral 30 minutes
This information can be updated until the beginning of the semester; information on the examination timetable is binding.

Learning materials

 
Main linkWebsite of the lecture/exercises
Only public learning materials are listed.

Groups

No information on groups available.

Restrictions

There are no additional restrictions for the registration.

Offered in

ProgrammeSectionType
Biology MasterElective Compulsory Master CoursesWInformation
Biology MasterElective Compulsory Master CoursesWInformation
Chemistry MasterComputational ChemistryWInformation
Chemical and Bioengineering MasterModeling and SimulationsWInformation
Computational Biology and Bioinformatics MasterBiophysicsWInformation
Doctorate Materials ScienceSoft Materials (MaP Doctoral School)WInformation
Computational Science and Engineering BachelorChemistryWInformation
Computational Science and Engineering MasterChemistryWInformation