Fundamentals of Molecular Modeling Field of study: Biophysics
Programme code: W4-S1BF19.2025

Module name: Fundamentals of Molecular Modeling
Module code: W4-BF-FA-S1-6-23-35
Programme code: W4-S1BF19.2025
Semester: summer semester 2027/2028
Language of instruction: Polish
Form of verification: exam
ECTS credits: 3
Purpose and description of the content of education:
The purpose of the module is to describe binding and non-binding interactions and to learn the method of optimization in simulations of molecular systems in particular: using the method of simple gradient, fastest gradient and coupled gradients, Metropolis algorithm. The student will learn classical computer simulations to obtain models of molecules and inter-molecular interaction potentials.
List of modules that must be completed before starting this module (if necessary): not applicable
Learning outcome of the module Codes of the learning outcomes of the programme to which the learning outcome of the module is related [level of competence: scale 1-5]
The student has basic knowledge of molecular dynamics simulations and the Monte Carlo method. [E1]
 W06 [1/5]
Knows the basics of molecular dynamics. [E2]
 W01 [1/5] W08 [1/5]
The student can determine the advantages and limitations of the known methods of computer simulations. [E3]
 W08 [1/5]
Is able to choose the model of interactions, the statistical ensemble and the parameters of classical simulations appropriate for the analyzed system. [E4]
 U06 [1/5]
The student can use available open programs to model simple molecules and simulate the dynamics of the system of atoms and molecules. [E5]
 U05 [1/5]
Form of teaching Number of hours Methods of conducting classes Assessment of the learning outcomes Learning outcomes
lecture [FZ1] 15 Formal lecture/ course-related lecture [a01]  exam E1 E2
laboratory classes [FZ2] 30 Working with a computer [d01] 
Laboratory exercise / experiment [e01]  		course work E3 E4 E5
The student's work, apart from participation in classes, includes in particular:
Name Category Description
Literature reading / analysis of source materials [a02] Preparation for classes
reading the literature indicated in the syllabus; reviewing, organizing, analyzing and selecting source materials to be used in class
Developing practical skills [a03] Preparation for classes
activities involving the repetition, refinement and consolidation of practical skills, including those developed during previous classes or new skills necessary for the implementation of subsequent elements of the curriculum (as preparation for class participation)
Getting acquainted with the syllabus content [b01] Consulting the curriculum and the organization of classes
reading through the syllabus and getting acquainted with its content
Implementation of an individual or group assignment necessary for course/phase/examination completion [c03] Preparation for verification of learning outcomes
a set of activities aimed at performing an assigned task, to be executed out of class, as an obligatory phase/element of the verification of the learning outcomes assigned to the course
Analysis of the corrective feedback provided by the academic teacher on the results of the verification of learning outcomes [d01] Consulting the results of the verification of learning outcomes
reading through the academic teacher’s comments, assessments and opinions on the implementation of the task aimed at checking the level of the achieved learning outcomes
Development of a corrective action plan as well as supplementary/corrective tasks [d02] Consulting the results of the verification of learning outcomes
reviewing and selecting tasks and activities enabling the elimination of errors indicated by the academic teacher, their verification or correction resulting in completing the task with at least the minimum passing grade
Attachments
Module description (PDF)
Information concerning module syllabuses might be changed during studies.
Syllabuses (USOSweb)
Semester Module Language of instruction
(no information given)