TCB Hands-on Workshop in San Francisco



  • Morning lecture sessions were held in the Social Room, and afternoon tutorial sessions were held in the Computer Training Center

Mon, 11/28: Introduction to Protein Structure and Dynamics, K. Schulten

08:30-08:45 Workshop Registration
08:45-09:00 Opening Remarks - Ralph Roskies
09:00-09:30 Overview of National Resource for Biomedical Supercomputing (NRBSC)
09:30-10:30 Molecular Graphics Perspective of Protein Structure and Function
Coffee Break
10:50-12:00 Molecular Dynamics Method
12:00-12:30 Daily Q & A
Lunch Break
13:30-13:45 Overview of Hands-on Sessions  
13:45-14:30 Molecular Graphics Tutorial
Coffee Break
14:45-17:00 Molecular Graphics Tutorial (continued)

Tue, 11/29: Statistical Mechanics of Proteins, K. Schulten

09:00-10:00 Molecular Dynamics with NAMD
10:00-11:00 Equilibrium Properties of Proteins
Coffee Break
11:15-12:15 Nonequilibrium Properties of Proteins
Daily Q & A
Group photo
Lunch Break
13:30-15:30 Molecular Dynamics Tutorial
Coffee Break
15:45-17:00 Molecular Dynamics Tutorial (continued)


Wed, 11/30: Parameters for Classical Force Fields, E. Tajkhorshid

09:00-10:00 Introduction to Classical Force Fields
10:00-11:00 Force Fields Parameterization
Coffee Break
11:15-12:15 Applications
12:15-12:30 Daily Q&A
Lunch Break
13:30-15:00 Paramaterizing a Novel Residue
Coffee Break
15:15-17:00 Topology File Tutorial

Thu, 12/1: Simulating Membrane Channels, E. Tajkhorshid

09:00-10:00 Transport in Membrane Channels
10:00-10:30 Nanotubes
10:30-10:40 Daily Q&A
Coffee Break/Evaluations
10:50-12:30 Nanotubes/IMD
Lunch Break
13:30- Open tutorial work time