Computer simulation of biological macromolecules

Academic: Dr. Sergiy Perepelytsya

The methods of computer simulations in the study of biological macromolecules will be considered. The course of lectures has 3 sections. The first section is devoted to the classical molecular dynamics. The second section is devoted to methods of modeling the electronic structure of molecules and quantum molecular dynamics. The third section is devoted to the study of the method of coarse-grained molecular dynamics. In this course, free softaware for modeling biological macromolecules (VMD, NAMD,) will be used.

Програма курсу
1. Fundamentals of the molecular dynamics method
2. Classical molecular dynamics
3. Coarse-grained molecular dynamics
4. Quantum molecular dynamics
Попердні вимоги

The final mark is formed by combining the marks for the assignments (40 points max) and the exam (60 points max).

Рекомендована література
  1. Schlick T., Molecular Modeling and Simulation. An Interdisciplinary Guide. New York: Springer-Verlag, Inc. – 2002. – 634 p.
  2. Atkins P., Friedman R. Molecular quantum mechanics, fourth edition. Oxford University Press (2005).
  3. Tutorial and user guide VMD.
  4. Tutorial and user guide NAMD.
  5. Tutorial and user guide MagiС.
  6. Tutorial and user guide cp2k.