Computational Biophysics Workshop - Atlanta, Mar. 21-25, 2011
Program
- Conference Room 102, Pettit Building
3/21: Introduction to Protein Structure and Dynamics - Klaus Schulten, Jeff Skolnick
08:00-08:30 | Participant Registration |
08:30-08:40 | Opening Remarks, Steve Harvey, Klaus Schulten |
08:40-10:10 | Introduction to Molecular Dynamics with VMD & NAMD, Klaus Schulten |
Coffee Break | |
10:30-12:00 | From Molecules to Cells - Whole Cell Simulations, Jeff Skolnick, CSSB |
12:00-12:20 | Q & A |
Lunch Break | |
13:20-15:00 | VMD Tutorial - Using VMD; NAMD Tutorial |
Coffee Break | |
15:20-17:00 | VMD Tutorial - Using VMD; NAMD Tutorial |
3/22: Statistical Mechanics of Proteins - Klaus Schulten
08:30-10:00 | Analysis of Equilibrium and Non-equilibrium Properties of Proteins with NAMD |
Coffee Break | |
10:20-11:50 | Exemplary Applications of VMD / NAMD in Modern Research |
11:50-12:10 | Q & A; Group picture |
Lunch Break | |
13:10-15:00 | Participant tutorial options: 1) NAMD Tutorial & Stretching Deca-alanine, or 2) Expert NAMD Set Tutorials*, or 3) Free Energy Set Tutorials** |
Coffee Break | |
15:20-17:00 | Participant tutorial options: 1) NAMD Tutorial & Stretching Deca-alanine, or 2) Expert NAMD Set Tutorials*, or 3) Free Energy Set Tutorials** |
3/23: Introduction to Bioinformatics - Zaida Luthey-Schulten
08:30-10:00 | Introduction to Evolutionary Concepts in Bioinformatics: MultiSeq in VMD |
Coffee Break | |
10:20-11:40 | Application of MultiSeq to Evolution of Translation Machinery |
11:40-12:00 | Q & A |
Lunch Break | |
13:00-15:00 | Participant tutorial options: 1) Basic Sequence Analysis: Aquaporins with the VMD MultiSeq Tool; or 2) Expert Sequence Analysis - Evolution of Translation Class I Aminoacyl-tRNA Synthetases: tRNA complexes - Evolution of Translation EF-Tu: tRNA - Evolution of Translation: The Ribosome; or 3) Participants work on their own projects |
Coffee Break | |
15:20-17:00 | Participant tutorial options: 1) Basic Sequence Analysis: Aquaporins with the VMD MultiSeq Tool; or 2) Expert Sequence Analysis - Evolution of Translation Class I Aminoacyl-tRNA Synthetases: tRNA complexes - Evolution of Translation EF-Tu: tRNA - Evolution of Translation: The Ribosome; or 3) Participants work on their own projects |
3/24: Parameters for Classical Force Fields - Emad Tajkhorshid
08:30-10:00 | Introduction to Topology, Parameters, and Structure Files |
Coffee Break | |
10:20-11:40 | Examples and Applications |
11:40-12:00 | Q & A |
Lunch Break | |
13:00-15:00 | Parameterizing a Novel Residue |
Coffee Break | |
15:20-17:00 | Topology File Tutorial |
3/25: Simulating Membrane Channels - Emad Tajkhorshid
08:30-10:00 | Modeling and Molecular Dynamics of Cellular Processes |
Coffee Break | |
10:20-11:40 | Nanotubes |
11:40-12:00 | Q & A |
Lunch Break | |
13:00-15:00 | Participant tutorial options: 1) Membrane Proteins & Simulation of Water Permeation Through Nanotubes, or 2) Expert NAMD Set Tutorials*, or 3) Free Energy Set Tutorials** |
Coffee Break | |
15:20-17:00 | Participant tutorial options: 1) Membrane Proteins & Simulation of Water Permeation Through Nanotubes, or 2) Expert NAMD Set Tutorials*, or 3) Free Energy Set Tutorials** |
Tutorial Options:
* Expert NAMD Set Tutorials:
- Shape-Based Coarse Graining
- User-Defined Forces in NAMD, or
** Free Energy Set Tutorials
-
A Tutorial to Set Up Alchemical Free Energy
Perturbation Calculations in NAMD
-
A Tutorial to Set Up Adaptive Biasing Force Calculations in
NAMD
Click here to see descriptions of tutorials listed in program.
Note: program subject to change.