Program

Locations:
  • Lectures and tutorials: Room U153, University of Southern Denmark (SDU), Campusvej 55
  • NOTE: On Monday, October 12, someone will be standing with a noticeable sign at SDU main entrance to accompany participants to the workshop room. Two escorts will be planned: one leaving at 8:05, the second one at 8:20. See this Venue Website for explicit instructions, maps, and bus schedules.

Monday, October 12: Introduction to Protein Structure and Dynamics - Klaus Schulten

08:00-08:30 Registration
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
12:20-14:00 Lunch Break
14:00-16:00 Tutorials
16:00-16:20 Coffee Break
16:20-18:00 Tutorials
Recommended tutorials: VMD Tutorial, NAMD Tutorial, qwikMD Tutorial

Tuesday, October 13: Statistical Mechanics of Proteins - Klaus Schulten

08:30-09:00 Coffee Break
09:00-10:30 Analysis of Equilibrium and Non-equilibrium Properties of Proteins with NAMD
10:30-10:50 Coffee Break
10:50-12:00 Applications of VMD / NAMD in Modern Research
12:00-12:20 Q & A; Group Picture
12:20-14:00 Lunch Break
14:00-16:00 Tutorials
16:00-16:20 Coffee Break
16:20-18:00 Tutorials
Recommended tutorials: NAMD Tutorial & Stretching Deca-alanine, User-Defined Forces in NAMD, Introduction to MD simulations of DNA-protein systems

Wednesday, October 14: Force Field Parametrization - Emad Tajkhorshid

08:30-09:00 Coffee Break
09:00-10:30 Introduction to Topology, Parameters, and Structure Files
10:30-10:50 Coffee Break
10:50-12:00 Examples and Applications / Force Field Toolkit
12:00-12:20 Q & A
12:20-14:00 Lunch Break
14:00-16:00 Tutorials
16:00-16:20 Coffee Break
16:20-18:00 Tutorials
Recommended tutorials: Parameterizing Small Molecules Using the Force Field Toolkit; Topology File Tutorial

Thursday, October 15: Simulating Membrane Proteins - Emad Tajkhorshid

08:30-09:00 Coffee break
09:00-10:30 Membrane Simulation with NAMD
10:30-10:50 Coffee Break
10:50-12:00 Transport in Membrane Channels
12:00-12:20 Q & A
12:20-14:00 Lunch Break
14:00-16:00 Tutorials
16:00-16:20 Coffee Break
16:20-18:00 Tutorials
Recommended tutorials: Membrane Proteins Tutorial

Friday, October 16: Free Energy Calculations - Chris Chipot

08:30-10:00 Introduction to Free-energy Calculations (part 1)
10:00-10:10 Coffee Break
10:10-11:30 Introduction to Free-energy Calculations (part 2)
11:30-12:00 Q & A
12:00-14:00 Lunch Break
14:00-16:00 Tutorials
16:00-16:20 Coffee Break
16:20-18:00 Tutorials
Recommended tutorials: Alchemical Free Energy Perturbation Calculations, Adaptive Biasing Force Calculations, (Recommended for advanced users: String Method with Swarms of Trajectories, Protein:Ligand Standard Binding Free Energies)


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".