Computational Biophysics Workshop - Atlanta, Nov. 3-7, 2014
Program
Locations:
- Lectures and tutorials: Parker H. Petit Institute for Bioengineering & Bioscience
Monday, November 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 |
Introduction to VMD and NAMD |
| 10:30-10:50 |
Coffee Break |
| 10:50-12:00 |
Analysis of Equilibrium and Non-equilibrium Properties of Proteins 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 |
Tuesday, November 4:
Free Energy Calculations - Chris Chipot
| 08:30-09:00 |
Continental breakfast |
| 09:00-10:30 |
Introduction to Free-energy Calculations (part 1) |
| 10:30-10:50 |
Coffee Break |
| 10:50-12:00 |
Introduction to Free-energy Calculations (part 2) |
| 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: |
Free Energy Tutorial; Adaptive Biasing Force Tutorial |
Wednesday, November 5:
Force Field Parameterization - Emad Tajkhorshid & James Gumbart
| 08:30-09:00 |
Continental breakfast |
| 09:00-10:30 |
Introduction to Topology, Parameters, and Structure Files - Emad Tajkhorshid |
| 10:30-10:50 |
Coffee Break |
| 10:50-12:00 |
Examples and Applications / Force Field Toolkit - James Gumbart |
| 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 a Novel Residue; Topology File Tutorial |
Thursday, November 6:
Simulating Membrane Proteins - Emad Tajkhorshid
| 08:30-09:00 |
Continental breakfast |
| 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, November 7:
Molecular Dynamics Flexible Fitting - James Gumbart
| 08:30-09:00 |
Continental breakfast |
| 09:00-10:30 |
Principles of Molecular Dynamics Flexible Fitting (MDFF) |
| 10:30-10:50 |
Coffee Break |
| 10:50-12:00 |
Fitting Cryo-EM Density Maps |
| 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: |
MDFF Tutorial |
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".
