Computational Biophysics Workshop - Bremen, Jun 16-20, 2014
Program
- Conference Hall, Campus Center, Campusring 1, Jacobs University Bremen
Mon, Jun. 16: Introduction to Protein Structure and Dynamics - Klaus Schulten
| 08:25-08:55 | Registration |
| 08:55-09:00 | Welcome and Brief Overview - Ulrich Kleinekathoefer |
| 09:00-09:10 | Opening Remarks |
| 09:10-11:00 | Structure and Sequence Analysis with VMD |
| 11:00-12:00 | Introduction to Molecular Dynamics with NAMD |
| Around 10:30 - Coffee Break | |
| 12:00-12:20 | Q & A |
| Lunch Break | |
| 14:00-18:00 | VMD Tutorial - Using VMD; NAMD Tutorial |
| Around 16:00 - Coffee Break | |
| 18:00+ | FIFA @ University Club |
| 19:00+ | Welcome Evening @ University Club |
Tue, Jun. 17: Introduction to Protein Structure and Dynamics - Klaus Schulten
| 09:00-10:30 | Analysis of Equilibrium and Non-equilibrium Properties of Proteins with NAMD |
| 10:30-12:00 | Applications of VMD / NAMD in Modern Research |
| Around 10:30 - Coffee Break | |
| 12:00-12:20 | Q & A |
| Lunch Break | |
| 14:00-18:00 | NAMD Tutorial; Stretching Deca-alanine; Simulation of Water Permeation Through Nanotubes |
| Around 16:00 - Coffee Break |
Wed, Jun. 18: Statistical Mechanics of Proteins - Klaus Schulten, Chris Chipot
| 09:00-10:00 | Modeling and Sequence Analysis of the Water Channel Aquaporin - Klaus Schulten |
| 10:00-12:00 | Introduction to Free-energy Calculations - Chris Chipot |
| Around 10:30 - Coffee Break | |
| 12:00-12:30 | Q & A; Group picture |
| Lunch Break | |
| 14:00-18:00 | Basic Sequence Analysis: Aquaporins with the VMD Multiseq Tool; Free Energy Set Tutorials: Alchemical Free Energy Perturbation Calculations in NAMD, Adaptive Biasing Force Calculations in NAMD |
| Around 16:00 - Coffee Break | |
| 18:00-19:30 | Dinner Break |
| 19:30-21:00 | Contributions from Participants |
Thu, Jun. 19: Parameters for Classical Force Fields - Emad Tajkhorshid
| 09:00-10:30 | Introduction to Topology, Parameters, and Structure Files |
| 10:30-12:00 | Examples and Applications |
| Around 10:30 - Coffee Break | |
| 12:00-12:20 | Q & A |
| Lunch Break | |
| 14:00-18:00 | Parameterizing a Novel Residue; Topology File Tutorial |
| Around 16:00 - Coffee Break |
Fri, Jun. 20: Simulating Membrane Channels - Emad Tajkhorshid and Ulrich Kleinekathöfer
| 09:00-10:30 | Membrane Simulation with NAMD - Emad Tajkhorshid |
| 10:30-12:00 | Transport through (biological) Nanopores - Ulrich Kleinekathöfer |
| Around 10:30 - Coffee Break | |
| 12:00-12:20 | Q & A |
| Lunch Break | |
| 14:00-18:00 | Membrane Proteins; Electrostatic Maps and Ion Conduction Tutorial. Optional: User-Defined Forces in NAMD; Shape-Based Coarse Graining; Alchemical Free Energy Perturbation Calculations in NAMD, Adaptive Biasing Force Calculations in NAMD; Simulation of Water Permeation Through Nanotubes |
| Around 16:00 - Coffee Break |
