Computational Biophysics Workshop - Odense, October 12-16, 2015
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".