TCBG Summer School - Urbana, Jun. 2-13, 2003
Locations
Morning lectures: Beckman Institute AuditoriumCoffee breaks: 1003 Beckman Institute
Afternoon and evening computer labs: 252 Everitt Lab / 406B1 Engineering Hall
campus map
Handouts
Running Simulations During the Afternoon Hands-on Sessions (html ,pdf)Four Ways to Run NAMD at SS03 (html, pdf)
Collaborative Exercises
EnergiesEchoes
Mon, 6/2: Introduction to Protein Structure and Dynamics (K. Schulten)
07:30-12:00 Registration
08:30-09:00 Welcome, Opening Remarks, and
Overview (pdf)
09:00-10:00 Molecular Graphics Perspective of
Protein Structure and Function (pdf)
Coffee Break
11:30-12:30 Equilibrium Properties of Proteins
(pdf)
12:30-12:45 Daily Q & A
Lunch Break (12:45-13:30 Staff
Meeting, 3169 BI )
13:45-14:30 Overview of Technical Resources (pdf) (T. Skirvin, K. Vandivort,
R. Brunner) [Beckman Institute Auditorium]
19:00-21:00 Free Session -- Model Your Own System (E. Villa,
J. Gullingsrud, M. Sotomayor, M. Dittrich)
Tue, 6/3: Statistical Mechanics of Proteins (I. Kosztin)
09:00-11:00 Registration
09:00-10:00 Equilibrium and Nonequilibrium
Properties of Proteins (pdf)
Coffee Break
11:30-12:30 Simulated Cooling of Proteins (pdf)
12:30-12:45 Daily Q & A
Lunch Break (12:45-13:30 Staff
Meeting, 3169 BI )
18:00-20:00 Banquet [Beckman Institute Atrium]
(closed event; nametags required)
Wed, 6/4: Steered Molecular Dynamics of Proteins (K. Schulten)
09:00-10:00 Introduction and Examples (pdf)
10:00-11:00 Mechanical Proteins (pdf)
Coffee Break
11:30-12:30 Determining Potentials (pdf)
12:30-12:45 Daily Q & A
Lunch Break (12:45-13:30 Staff
Meeting, 3169 BI )
19:00-21:00 Free Session -- Model Your Own System
(A. Aksimentiev, J. DeSouza, B. Isralewitz, J. Cohen)
Thu, 6/5: Simulating Membrane Channels (E. Tajkhorshid)
09:00-10:00 Introduction and Examples (pdf)
10:00-11:00 Transport in Aquaporins (pdf)
Coffee Break
11:30-12:30 Nanotubes (pdf)
12:30-12:45 Daily Q & A
12:45 Summer School Photo
Lunch Break (12:45-13:30 Staff
Meeting, 3169 BI )
17:30-19:00 Demonstration of Aquaporin channel
and Haptic Device IMD (3 demos) [3151 BI]
19:00-21:00 Free Session -- Model Your Own System (D. Lu, F. Zhu)
Fri, 6/6: Quantum Chemistry of Proteins (T. Martinez)
09:00-10:00 Introduction and Examples (pdf)
10:00-11:00 Ab Initio and Semiempirical Quantum
Chemistry (pdf)
Coffee Break
11:30-12:30 QM/MM Methods and Direct Dynamics (pdf)
12:30-12:45 Daily Q & A
Lunch Break (12:45-13:30 Staff
Meeting, 3169 BI )
15:45-17:00 Hands-on -- Computational
Determination of Proton Affinities (html,
pdf)
(M. Dittrich, S. Olsen)
19:00-21:00 Free Session -- Model Your Own System
(C. Kanchanawarin, M. Gao)
Sat, 6/7
Bus Trip to Chicago (Optional, Not Funded by School, Sign up Early)Sun, 6/8
14:00-21:00 Free Session -- Model Your Own System
Mon, 6/9: Parameters for Classical Force Fields (Z. Schulten)
09:00-10:00 Introduction and Examples (pdf)
10:00-11:00 Introduction to Classical Force
Fields (pdf)
Coffee Break
11:30-12:30 Methods of Parameterization (pdf)
12:30-12:45 Daily Q & A
Lunch Break (12:45-13:30 Staff
Meeting, 3169 BI )
14:30-15:30 Hands-on -- System Setup of HisH with
the Molecular Modeling Package Moe (html, pdf)
(R. Amaro, F. Autenrieth, R. Braun)
15:45-17:00 Hands-on -- Semiempirical Parameter
Generation with Spartan (html, pdf)
(R. Amaro, F. Autenrieth, R. Braun)
17:30-19:00 Demonstration of Aquaporin channel
and Haptic Device IMD (3 demos) [3151 BI]
19:00-21:00 Free Session - Model Your Own System (G. Zheng,
S. Kumar)
Tue, 6/10: Bioinformatics of Proteins (Z. Schulten)
10:00-11:00 Sequence and Structure Alignment
Algorithms (pdf)
Coffee Break
11:30-12:30 Sequence and Structural Analysis
Tools on the Web (pdf)
12:30-12:45 Daily Q & A
Lunch Break (12:45-13:30 Staff
Meeting, 3169 BI )
14:30-15:30 Hands-on -- Bioinformatics
Introduction on Class II tRNA Synthetases (html, pdf)
(F. Autenrieth, B. Isralewitz, T. Pogorelov)
15:45-17:00 Hands-on -- Sequence and Structural
Alignment Methods (html, pdf)
(F. Autenrieth, B. Isralewitz, T. Pogorelov)
19:00-21:00 Free Session -- Model Your Own System (D. Hardy,
F. Khalili)
Wed, 6/11: Simulation of Lipids (M. Klein); Parallel Computing (L. Kale)
08:55-09:00 Entries for Beauty Contest are due
09:00-10:00 Atomic Level Simulation of Membranes
(pdf) (M. Klein)
10:00-11:00 Coarse Grained Modeling of Lipid
Phases (pdf)
(M. Klein)
Coffee Break
11:30-12:30 Introduction to Parallel Computing
Issues (pdf)
(L. Kale)
12:30-12:45 Daily Q & A
12:45-12:50 Announcement of Beauty Contest
Finalists
Lunch Break (12:50-13:30 Staff
Meeting, 3169 BI )
14:30-15:30 Hands-on -- Case Studies in Effective
Parallelization of MD Simulations (pdf) (L. Kale)
15:45-16:30 Optional - Introductory Lessons on
Cluster Building (pdf);
Choose-up for Section 1, 2, or 3 (T. Skirvin, J. Stone, J. Phillips)
16:30-18:30 Optional - Hands-on -- Build Your Own
Cluster 1 (html,
pdf)
(T. Skirvin, J. Stone, J. Phillips) (5602 BI)
19:00-21:00 Free Session -- Model Your Own System
(R. Braun, D. Brandon)
Thu, 6/12: Numerical Algorithms (T. Schlick, R. Skeel)
Coffee Break
12:30-12:45 Feedback Forms
Lunch Break (12:45-13:30 Staff
Meeting, 3169 BI )
14:30-15:30 Hands-on -- Numerical Laboratory (pdf)
(D. Hardy, R. Engle, J. Marriott, W. Wang)
15:30-17:30 Optional - Hands-on -- Build Your Own
Cluster 2 (html,
pdf)
(T. Skirvin, J. Stone, J. Phillips) (5602 BI)
17:30-19:30 Optional - Hands-on -- Build Your Own
Cluster 3 (html,
pdf)
(T. Skirvin, J. Stone, J. Phillips) (5602 BI)
15:30-17:00 NCSA
Cave Tours (6 Tours) [3510 BI]
19:30-21:00 Beauty Contest
[Beckman Institute Auditorium]
The certificate of the summer school will be handed out.
The certificate of the summer school will be handed out.
Fri, 6/13: Modeling Large Systems (K. Schulten)
09:00-10:00 Molecular Machines of the Living Cell
(pdf)
10:00-11:00 Light Harvesting in Photosynthesis
(pdf)
Coffee Break
11:30-12:00 ATP Synthase (pdf)
12:00-12:15 Daily Q & A
12:15-12:45 Concluding Remarks
Lunch Break (12:45-13:30 Staff
Meeting, 3169 BI )
13:00-14:30 NCSA
Cave Tours (6 Tours) [3510 BI]