Computational Biophysics Workshop - Urbana, Oct. 22-26, 2012
Program
- Lectures: Room 3269 of the Beckman Institute
- Tutorials: Room 3269 and TCBG Innovation Areas I & II at Beckman
Mon, Oct. 22: Introduction to Protein Structure and Dynamics - Klaus Schulten
08:30-09:00 | Registration |
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 |
12:00-12:20 | Q & A |
Lunch Break | |
14:00-16:00 | VMD Tutorial - Using VMD; NAMD Tutorial |
Coffee Break | |
16:15-18:00 | VMD Tutorial - Using VMD; NAMD Tutorial |
Dinner Break | |
19:30-20:00 | VMD from the Developer's Perspective - John Stone |
20:00-20:30 | Computational Investigation of DNA Detection Using Graphene Nanopores - Chaitanya Sathe |
20:30-21:00 | Workshop Participant Short Lecture: Atomistic Molecular Dynamics Simulation of Poliovirus - Jason Roberts |
Tue, Oct. 23: 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: |
Coffee Break | |
16:15-18:00 | Participant tutorial options: |
Dinner Break | |
19:30-20:00 | NAMD from the Developer's Perspective - Jim Phillips |
20:00-20:30 | Molecular Dynamics Simulation of Protein Folding - Yanxin Liu |
20:30-21:00 | Workshop Participant Short Lectures: |
21:00-21:30 | Cloud Computing Opportunities for Computational Investigators (Amazon) - Ryan McGreevy |
Wed, Oct. 24: Statistical Mechanics of Proteins - Klaus Schulten
09:00-10:00 | Analysis of Equilibrium and Non-equilibrium Properties of Proteins with NAMD |
10:00-10:45 | Applications of VMD / NAMD in Modern Research |
Coffee Break | |
11:00-12:00 | Introduction to GPU Accelerated NAMD Simulation - K. Schulten, R. McGreevy |
12:00-12:30 | Q & A; Group picture |
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** 4) GPU Accelerated Molecular Dynamics and Visualization Tutorial |
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** 4) GPU Accelerated Molecular Dynamics and Visualization Tutorial |
Thu, Oct. 25: 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 |
Dinner Break | |
20:00-20:30 | Molecular Dynamics Flexible Fitting - Ryan McGreevy |
20:30-21:00 | Structural Analyses of the Ribosome by Hybrid Approach - Yan Chan |
21:00-21:30 | Workshop Participant Short Lecture: Deprotonation of D96 in Bacteriorhodopsin Opens the Proton Uptake Pathway - Ting Wang |
Fri, Oct. 26: 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** |
Dinner Break | |
20:00-21:30 | Final Presentations by Workshop Participants: |
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 by NIH P41-RR005969 "Resource for Macromolecular Modeling and Bioinformatics".