DEPARTMENT OF PHYSICAL CHEMISTRY

Course: Molecular modeling and simulations

Number: 403433
Semester : 9th
Weekly load and assessment: 1/1 Ex
Credits: 3
Language: Czech, English
Lecturer: RNDr.Jiri Kolafa CSc.
This instruction is provided at the Department of Physical Chemistry

Contents:
  1. Statistical thermodynamics: ensembles, probabilities of states
  2. Models: lattice and continuous, description of fluids, proteins
  3. Molecular dynamics: integration of equations of motion (Verlet, Gear)
  4. MD: isothermal and isobaric ensembles
  5. MD: rigid molecules, molecules with rigid bonds (SHAKE)
  6. Monte Carlo: MC integration, Markov chains, Metropolis sampling
  7. Random numbers: algorithms, continuous and discrete distributions
  8. MC: rigid molecules, MC in other ensembles
  9. MC: non-Boltzmann sampling
  10. Computer experiment: choice of method and conditions, simulation start
  11. Periodic boundary conditions, long range forces
  12. Measurements, statistical analysis of time series, error estimation
  13. Entropic quantities (thermodynamic integration, Widom)
  14. MD: kinetic quantities, equilibrium and non-equilibrium methods