Molecular Modeling 1200-2RMODEL1M
The role of molecular modeling in science. Basic techniques of molecular mechanics and their relations with physical experiments. Selected software packages and databases. Molecular dynamics - algorithms and stability of MD. Brownian dynamics. The problem of the finite size of model systems. Force fields in MD. Monte Carlo methods. Various statistical ensembles in MC. Generalized ensemble MC. Replica Exchange MC. Applications of various techniques of molecular modeling to the global energy minimum problem. Studying phase transitions and diffusion - selection of methods and boundary conditions -critical slow down. Mesoscopic and reduced models. Modeling of macromolecules and large biomolecular systems. Ligand docking. Membranes. Reduction of conformational space. Potentials of mean force and statistical potentials. Multiscale modeling. Realtions between Monte Carlo dynamics and classical molecular dynamics
Type of course
Mode
Course coordinators
Learning outcomes
Basic knowledge of molecular modeling methods, including energy minimization, Molecular Dynamics, molecular Monte Carlo. Practical skils in applications of molecular modeling in physical chemistry and in organic chemistry.
Assessment criteria
Written test, containing 15 closed questions and 5 open questions, conducted off-line (in a class room) or an oral exam - possibly online
Bibliography
1. P. von Rague Schleyer, Encyclopedia of Compuational Chemistry, Wiley 1998
2. K. Binder, D. W. Heermann, Monte Carlo Simulations in Statistical Physics, Springer 2002
3. D. Frenkel, B. Smit, Understanding Molecular Simulation, Academic Press, 2001
Additional information
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