Fundamentals of Molecular Modeling Field of study: Biophysics
Programme code: W4-S2BFA21.2022

Module name: Fundamentals of Molecular Modeling
Module code: W4-2BF-MB-21-22
Programme code: W4-S2BFA21.2022
Semester:
  • winter semester 2025/2026
  • winter semester 2024/2025
  • winter semester 2023/2024
Language of instruction: English
Form of verification: exam
ECTS credits: 5
Description:
During the lecture, the student becomes acquainted with the following issues: Molecular mechanics: -Description of binding and non-binding interactions. -Force fields: MMFF94, GAFF and GROMACS. -Optimization methods: simple gradient method, fastest gradient and conjugate gradients, Metropolis algorithm. Classic computer simulations: -Models of molecules and potentials of intermolecular interactions. Deterministic computer simulation methods - isolated molecular systems and extended systems (periodic boundary conditions, nearest image convention, spherical truncation, shifted potential), equations of motion, methods of solving difference equations, dynamics with constraints, long-range interactions, molecular dynamics for a microcanonical ensemble, canonical and isobaric-isothermal; mean values and fluctuations, thermodynamic quantities, temporal correlation functions, correlation times and transport coefficients, structural properties (binary decomposition function, static structure factor), long-range potential energy and pressure corrections. -Stochastic computer simulation methods - Monte Carlo method (Metropolis method, simulations for the canonical ensemble). During the laboratory classes free software such as GROMACS, Avogadro, VMD, NAMD, will be used to: -Constructing a given molecule and determining its most probable conformation. -Conducting a molecular dynamics simulation of a system of atoms. -Conducting molecular dynamics simulations of a system of simple molecules
Prerequisites:
(no information given)
Key reading:
(no information given)
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]
Has basic knowledge of molecular dynamics simulation and Monte Carlo method [MB_22_1]
 KBF_W08 [5/5]
Student knows the basics of molecular dynamics [MB_22_2]
 KBF_W08 [5/5]
Student can identify the advantages and limitations of known computer simulation methods [MB_22_3]
 KBF_W08 [5/5]
Student can choose the proper model of the interaction, statistical set and parameters of classical simulations appropriate for the analyzed system [MB_22_4]
 KBF_U02 [4/5]
He can use the available programs with open access to model simple molecules and simulate the dynamics of the system of atoms and molecules [MB_22_5]
 KBF_U06 [4/5]
Type Description Codes of the learning outcomes of the module to which assessment is related
exam [MB_22_w_1]
written exam/oral exam
 MB_22_1 MB_22_2 MB_22_3 MB_22_4 MB_22_5
credit [MB_22_w_2]
Two written tests. Constructing the starting configuration of a given molecule and optimizing its structure. Preparation of a system of atoms/molecules for a given density and thermodynamic conditions and starting a molecular dynamics simulation of such a system. The credit grade will be the arithmetic mean of the test marks on a scale of 2-5.
 MB_22_1 MB_22_2 MB_22_3 MB_22_4 MB_22_5
Form of teaching Student's own work Assessment of the learning outcomes
Type Description (including teaching methods) Number of hours Description Number of hours
lecture [MB_22_fs_1]
Detailed discussion by the lecturer of the issues listed in the table "module description" using the table and / or multimedia presentations
 30
Work with the textbook; supplementary reading
 60 exam [MB_22_w_1]
laboratory classes [MB_22_fs_2]
Getting to know the available software, constructing molecules, selecting the force field and determining the equilibrium configuration. Designing a system of molecules using the implemented force fields and simulating the molecular dynamics of this system
 30
Acquiring knowledge from lectures
 45 credit [MB_22_w_2]
Attachments
Module description (PDF)
Information concerning module syllabuses might be changed during studies.
Syllabuses (USOSweb)
Semester Module Language of instruction
(no information given)