Program

Location Room 115, Energy Biosciences Building University of California Berkeley 2151 Berkeley Way, Berkeley, CA 94704

Monday, August 3: Introduction to Protein Structure and Dynamics - Klaus Schulten

08:00-08:30 Registration and Continental Breakfast
08:30-09:00 Welcome, Brief Overview, and Opening Remarks
09:00-10:30 Structure and Sequence Analysis with VMD
10:30-10:50 Coffee Break
10:50-12:00 Introduction to Molecular Dynamics with NAMD
12:00-12:20 Q & A
12:20-13:30 Lunch Break
13:30-15:30 Tutorials
15:30-15:50 Coffee Break
15:50-17:00 Tutorials
Recommended tutorials: VMD Tutorial, NAMD Tutorial

Tuesday, August 4: Statistical Mechanics of Proteins - Klaus Schulten

08:00-08:30 Continental Breakfast
08:30-10:00 Analysis of Equilibrium and Non-equilibrium Properties of Proteins with NAMD
10:00-10:20 Coffee Break
10:20-11:30 Applications of VMD / NAMD in Modern Research
11:30-11:50 Q & A; Group Picture
11:50-13:00 Lunch Break
13:00-15:00 Tutorials
15:00-15:20 Coffee Break
15:20-17:00 Tutorials
Recommended tutorials: NAMD Tutorial & Stretching Deca-alanine, User-Defined Forces in NAMD

Wednesday, August 5: Force Field Parameterization - Emad Tajkhorshid

08:00-08:30 Continental Breakfast
08:30-10:00 Introduction to Classical Force Fields - Topology, Parameters, and Structure Files
10:00-10:20 Coffee Break
10:20-11:30 Examples and Applications / Force Field Toolkit
11:30-11:50 Q & A
11:50-13:00 Lunch Break
13:00-15:00 Tutorials
15:00-15:20 Coffee Break
15:20-17:00 Tutorials
Recommended tutorials: Topology File Tutorial, Parametrizing a Novel Residue Tutorial

Thursday, August 6: Molecular Dynamics Flexible Fitting Methods - Ryan McGreevy

08:00-08:30 Continental Breakfast
08:30-10:00 Molecular Dynamics Flexible Fitting Method I
10:00-10:20 Coffee Break
10:20-11:30 Molecular Dynamics Flexible Fitting Method II
11:30-11:50 Q & A
11:50-13:00 Lunch Break
13:00-15:00 Tutorials
15:00-15:20 Coffee Break
15:20-17:00 Tutorials
Recommended tutorials: MDFF Tutorial, Structure check Tutorial

Friday, August 7: Introductions to Evolutionary Concepts, Network Analysis, and Cell Simulations - Zan Luthey-Schulten

08:00-08:30 Continental Breakfast
08:30-10:00 Applications of Evolutionary Algorithms and Network Analysis in MultiSeq/VMD to Translation
10:00-10:20 Coffee Break
10:20-11:30 Introduction to Simulations of Bacterial Cells
11:30-11:50 Q & A
11:50-13:00 Lunch Break
13:00-15:00 Tutorials
15:00-15:20 Coffee Break
15:20-17:00 Tutorials
Recommended tutorials: Lattice Microbe Simulations. Other tutorials of interest: Aquaporins with the VMD MultiSeq Tool, Evolution of Translation: Class-I aminoacyl-tRNA synthetases, Evolution of Translation: EF-Tu, Evolution of Translation: Ribosome, Dynamical Network Analysis


Click here to see descriptions of tutorials listed in program.

Note: program subject to change. Workshop supported by NIH 9P41GM104601 "Center for Macromolecular Modeling and Bioinformatics".