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**
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**
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**
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**
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
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
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".