Computational Biophysics Workshop - Champaign, Aug. 10-14, 2009
Program
Location:
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Technology Room (just past elevators in hotel lobby)
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Beckman Institute, Room 3151 (Evenings, Tuesday and Thursday afternoons)
Sun, 8/09: Meet in iHotel lobby at 8:00 pm, drinks at Houlihan's 8:00-10:00 pm
Mon, 8/10: Introduction to Protein Structure and Dynamics
| 08:30-09:00 | Continental Breakfast |
| 09:00-09:10 | Opening Remarks |
| 09:10-10:40 | Structure and Sequence Analysis with VMD |
| Coffee Break | |
| 11:00-12:00 | Introduction to Molecular Dynamics with NAMD |
| 12:00-12:30 | VMD 1.8.7 - Key features of recent release; John Stone |
| Lunch Break | On your own for lunch |
| 14:00-15:30 | VMD Tutorial - Using VMD; NAMD Tutorial |
| Coffee Break | |
| 16:00-18:00 | NAMD Tutorial |
| Dinner Break | Transport to Bread Company, dinner |
| 20:00-23:00 | Open lab time at Beckman Institute - work on your own project; transport back to iHotel provided |
Tue, 8/11: Statistical Mechanics of Proteins
| 08:30-09:00 | Continental Breakfast |
| 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 |
| 12:00-12:30 | NAMD 2.7 - Key features of upcoming release; Chris Harrison |
| Lunch Break | Transport to Beckman Institute, lunch |
| Note: tutorial sessions will be held at the Beckman Institute (go to Room 3151) | |
| 14:00 - 15:00 | Demos of research by Theoretical & Computational Biophysics Group (TCBG) members (two half-hour sessions, Room 3151) |
| 15:00-16:00 | Participant tutorial options: 1) NAMD Tutorial & Stretching Deca-alanine, or 2) Expert NAMD Set Tutorials: - Shape-Based Coarse Graining - User-Defined Forces in NAMD, or 3) 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 |
| Coffee Break | |
| 16:15-18:00 | Participant tutorial options: 1) NAMD Tutorial & Stretching Deca-alanine, or 2) Expert NAMD Set Tutorials: - Shape-Based Coarse Graining - User-Defined Forces in NAMD, or 3) 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 |
| Dinner Break | On your own in campus area |
| 20:00-23:00 | Open lab time at Beckman Institute - work on your own project; transport back to iHotel provided |
Wed, 8/12: Introduction to Bioinformatics
| 08:30-09:00 | Continental Breakfast |
| 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 |
| 12:00-12:30 | Sequence analysis in VMD 1.8.7 - Key features; Kirby Vandivort |
| Lunch Break | On your own for lunch |
| 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 |
| Dinner Break | Transport to downtown Champaign, dinner place to be suggested |
| 20:00-23:00 | Open lab time at Beckman Institute - work on your own project; transport back to iHotel provided |
Thu, 8/13: Parameters for Classical Force Fields
| 08:30-09:00 | Continental Breakfast |
| 09:00-10:30 | Introduction to Topology, Parameters, and Structure Files |
| Coffee Break | |
| 10:50-12:00 | Examples and Applications |
| 12:00-12:30 | GPU accelerated NAMD 2.7; Jim Phillips |
| Lunch Break | Transport provided to Beckman, lunch |
| Note: tutorial sessions will be held at the Beckman Institute (go to Room 3151) | |
| 14:00-15:00 | Demos of research by TCBG members (two half-hour sessions, Room 3151) |
| 15:00-16:30 | Parameterizing a Novel Residue; Topology File Tutorial |
| Coffee Break | |
| 16:45-18:00 | Simulation of Water Permeation through Nanotubes |
| Dinner Break | On your own in campus area |
| 20:00-23:00 | Open lab time at Beckman Institute - work on your own project; transport back to iHotel provided |
Fri, 8/14: Simulating Membrane Channels
| 08:30-09:00 | Continental Breakfast |
| 09:00-10:30 | Introduction and Examples |
| Coffee Break | |
| 10:50-12:00 | Transport in Aquaporins; Nanotubes |
| 12:00-12:30 | Highlights of VMD plugins; Robert Brunner |
| Lunch Break | On your own for lunch |
| 14:00 -16:30 | Participant tutorial options: 1) Membrane Proteins Tutorial; or 2) Expert NAMD Set Tutorials: - Shape-Based Coarse Graining - User-Defined Forces in NAMD; or 3) 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 |
| Coffee Break | |
| 16:45-18:00 | Participant tutorial options: 1) Membrane Proteins Tutorial; or 2) Expert NAMD Set Tutorials: - Shape-Based Coarse Graining - User-Defined Forces in NAMD; or 3) 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 |
| Dinner Break | On your own at iHotel |
| 20:00-23:00 | At Beckman, farewell reception and "Protein Beauty Contest" (optionally present your own project, 5 minutes lectures, win a prize!); transport back to iHotel provided |
Note: program subject to change.
