Workshop on Computer Simulations of Macromolecular Systems (2 days workshop)
Hiqmet Kamberaj, PhD
Faculty of Engineering
International Balkan University
Content & Objectives: This workshop aims to help the students to understand and apply the computer simulation methods, such as molecular dynamics, in real systems in the field of biophysics and nanotechnology. In particular, in this workshop, we shall discuss the molecular systems in the context of classical mechanics, their dynamics, molecular dynamics method; applications of the technique in real systems; statistical analysis of the results; computer programs used to perform molecular dynamics simulations. During this workshop, the students shall perform laboratory work in a computer environment to practice the applications of the molecular dynamics method in real systems.
This workshop is a necessary reference to understand the physics and mechanisms of development of many processes, which happen in the molecular systems in general, and macromolecular systems.
Work in a Laboratory
|Knowing how to use NAMD and/or CHARMM program scripting.||2|
|Introduction to Visualisation of Macromolecules using VMD program.||2|
|Energy minimization of C2 fragment of protein G.||2|
|Introduction to Molecular Dynamics simulations in vacuum and solutions.||2|
|Analysis of molecular dynamics simulations.||2|
|Normal mode analysis.||2|
|H. Kamberaj||Molecular Dynamics Simulations in Statistical Physics. Theory and Applications||2020, Springer Nature, Switzerland, Scientific Computation Series.|
|H. Kamberaj||Practical Guide to Macromolecular Simulations – A Handbook||2020/2021.|
Up to 10 Computers from IBU lab (any operating system; however, Linux will be preferred). Alternatively, students can bring their own laptops.
For (my) students of the University of Tetovo and IBU is free. Other students will get free materials indicated in References; therefore, the fees can be decided.