BLU 604E - Adv.Ana.Tec.for Mol.Dyn.Simu.

Course Objectives

1)Teaching applications of MD simulation in biomembrane applications
2)Teaching advanced methods for analyzing MD simulation trajectories
3)Teaching usage of programs and codes developed for analyzingMD simulation results

Course Description

Applications of MDSimulationsin biomembrane dynamics and function studies.Performing MD Simulations with NAMD program.VMD: a MD simulation analysis program.Time series analysis of basic features: Hydrogen bond, secondary structure, angle and distance.Root Mean Square Deviation (RMSD) andRoot Mean Square Fluctuation (RMSF) calculations.Radial distribution function (RDF) and radius of gyration calculations.Principal component analysis of MD trajectory.Cross-correlation analysis.Elastic Network analysis of MD trajectories.Methods for analyzing simulations of Biomembranes and Membrane proteins.Density and diffusion calculations.Interaction Energy calculations of MD trajectories.MD simulation analysis using Markov State models-1.MD simulation analysis using Markov State models-2