270274 UE Computer laboratory: Computersimulation of Biomolecules (2009S)
Continuous assessment of course work
Labels
Die Uebung findet geblockt taeglich vom 9.-20.3.2009, 11-14h, in den Raeumen des Instituts für Computergestützte Biologische Chemie (Währinger Strasse 17, Parterre) statt.
Details
Information
Aims, contents and method of the course
Preparing PDB files for use with CHARMM; manipulating protein and peptide structures with CHARMM; energy calculation and minimization; introduction to molecular dynamics; analysis of trajectories - comparison to experimentally accessible properties; methodological exercises; overview of the present "state of the art" (PME, NPT-simulations, ...); setting up of a solvated system. Practical applications: Analyzing a pre-calculated trajectory of a solvated protein; illustrating free energy simulations by a gas phase example; use of (NOE) restraints in MD simulations; structure refinement using restraints; calculating NMR data from a trajectory. See also http://www.mdy.univie.ac.at/lehre/nmr_sim.html
Assessment and permitted materials
Continuous evaluation of students' participation
Minimum requirements and assessment criteria
Introduction to biomolecular simulation using the program CHARMM
Examination topics
Practical exercises using CHARMM
Reading list
Association in the course directory
CHE II-7, MMB W-3
Last modified: Fr 31.08.2018 08:55