Computational Biophysics Workshop - Pittsburgh, May 10-14, 2010
Program
- Pittsburgh Supercomputing Center, 300 S. Craig St., Pittsburgh, PA - in the Oakland neighborhood of Pittsburgh (map)
- Lectures will be held in Room #103
- Tutorial sessions will be held in Room #110
- Meals will be served in Room #102
Mon, 5/10: Introduction to Protein Structure and Dynamics - Klaus Schulten
08:00-08:30 | Registration and Continental Breakfast |
08:30-09:00 | Welcome and Brief Overview of the NRBSC - Markus Dittrich |
09:00-09:10 | Opening Remarks |
09:00-10:40 | Structure and Sequence Analysis with VMD |
Coffee Break | |
11:00-12:00 | Introduction to Molecular Dynamics with NAMD |
12:00-12:20 | Q & A |
Lunch Break | |
13:30-14:00 | Brief Overview of PSC - PSC Allocations Staff |
14:00-16:00 | VMD Tutorial - Using VMD; NAMD Tutorial |
Coffee Break | |
16:15-18:00 | VMD Tutorial - Using VMD; NAMD Tutorial |
Tue, 5/11: Statistical Mechanics of Proteins - Klaus Schulten
09:00-10:30 | Analysis of Equilibrium and Non-equilibrium Properties of Proteins with NAMD |
Coffee Break | |
10:50-12:00 | Exemplary Applications of VMD / NAMD in Modern Research |
12:00-12:20 | Q & A |
Lunch Break | |
14:00-16:00 | Participant tutorial options: 1) NAMD Tutorial & Stretching Deca-alanine, or 2) Expert NAMD Set Tutorials*, or 3) Free Energy Set Tutorials** |
Coffee Break | |
16:15-18:00 | Participant tutorial options: 1) NAMD Tutorial & Stretching Deca-alanine, or 2) Expert NAMD Set Tutorials*, or 3) Free Energy Set Tutorials** |
Wed, 5/12: Parameters for Classical Force Fields - Emad Tajkhorshid
09:00-10:30 | Introduction to Topology, Parameters, and Structure Files |
Coffee Break | |
10:50-12:00 | Examples and Applications |
12:00-12:20 | Q & A |
Lunch Break | |
14:00-16:30 | Parameterizing a Novel Residue |
Coffee Break | |
16:45-18:00 | Topology File Tutorial |
Thu, 5/13: Simulating Membrane Channels - Emad Tajkhorshid
09:00-10:30 | Introduction and Examples |
Coffee Break | |
10:50-12:00 | Transport in Aquaporins; Nanotubes |
12:00-12:20 | Q & A |
Lunch Break | |
14:00 -16:00 | 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 | |
16:15-18:00 | Participant tutorial options: 1) Membrane Proteins & Simulation of Water Permeation Through Nanotubes, or 2) Expert NAMD Set Tutorials*, or 3) Free Energy Set Tutorials** |
Fri, 5/14: Introduction to Bioinformatics - Zaida Luthey-Schulten
09:00-10:30 | Introduction to Evolutionary Concepts in Bioinformatics: MultiSeq in VMD |
Coffee Break | |
10:50-12:00 | Application of MultiSeq to Evolution of Translation Machinery |
12:00-12:20 | Q & A |
Lunch Break | |
14:00-16:00 | 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 | |
16:15-18:00 | 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 |
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. Workshop supported in part by NIH P41-RR005969 "Resource for Macromolecular Modeling and Bioinformatics".