Very Large System Simulation Workshop

Program

Locations:
  • Lectures: Room 3269 of the Beckman Institute
  • Tutorials: Room 3269 and TCBG Innovation Courtyards I and II at Beckman

Mon, August 11: Preparing Large-Scale Simulations

08:30-09:00 Registration
09:00-10:00 Opportunities for Large System Simulations Today: Science, Software, Hardware - Klaus Schulten
10:00-11:00 Large System Assembly from Multi-Resolution Crystallographic and Cryo-EM Data - Till Rudack
Coffee Break  
11:20-12:20 Case Study: HIV Capsid - Juan Perilla
Lunch Break  
14:00-14:30 Setting Up Large Simulations with VMD: Solvate, Ionize, Structure and Topology Files - Boon Chong Goh, Danielle Chandler
14:30-15:00 Running Large Simulations with NAMD: Memory Optimized Version - Jim Phillips, Kirby Vandivort, Barry Isralewitz
Coffee Break  
15:15-17:30

Hands-on Training:
- Setting Up Large Simulations with VMD
- Running Large Simulations with NAMD
17:30-18:00 Questions and Answers

 

Tue, August 12: Building Multi-Protein Complexes

09:00-10:00 Determining Large Structures through Hybrid Methods using Molecular Dynamics Flexible Fitting - Ryan McGreevy, Boon Chong Goh, Keith Cassidy
10:00-11:00 Case Study: Photosynthetic Membrane - Danielle Chandler
Coffee Break  
11:20-12:30 Presentation of Participant Projects
Lunch Break  
13:30-13:45 Preparing Large-Scale Simulations: Virus Modeling - Boon Chong Goh, Keith Cassidy, Yi Zhang
13:45-16:30 Hands-on Training: Modeling a Large Virus System - Boon Chong Goh, Keith Cassidy, Yi Zhang
Coffee Break  
16:45-17:00

Questions and Answers
17:00-18:00 Presentation of Participant Projects

 

Wed, August 13: Analysis of Multi-Protein Complexes

09:00-10:00 Case Study: Sensory Array of Bacteria - Keith Cassidy
10:00-11:00 NAMD Tuning on Petascale Supercomputers - Jim Phillips
Coffee Break  
11:20-12:20 Analyzing Large Scale Simulations: Electrostatics, Interaction Energies, Radial Distribution, Solvent Accessible Surface Area, Contacts, Principle Component Analysis - Juan Perilla
Lunch  
13:30-16:30 Hands-on Training: Analyzing Large Scale Simulations with VMD - Juan Perilla, Barry Isralewitz, Till Rudack
Coffee Break  
16:45-17:30 Hands-on Training: Analyzing Large Scale Simulations with VMD - Juan Perilla, Barry Isralewitz, Till Rudack
17:30-18:00

Questions and Answers
18:00- Workshop Dinner

 

Thu, August 14: Guest Lectures and Open Lab Time

09:00-10:00 Blue Waters Lecture [title pending] - Bill Kramer, NCSA
10:00-12:00 Blue Waters Tour - Trish Barker, Public Affairs Coordinator, National Center for Supercomputing Applications
Lunch  
13:30-14:30 "An Atomistic Simulation of the Entire Influenza Virion Coat" - Jacob Durrant, Amaro Lab, U. California at San Diego
14:30-16:00 Open Lab Time
Coffee Break


16:15-18:00

Open Lab Time

 

Fri, August 15: Open Lab Time

09:00-11:00 Open Lab Time
Coffee Break  
11:15-12:20 Open Lab Time
Lunch  
14:00-16:00

Open Lab Time
Coffee Break  
16:15-18:00

Open Lab Time

 

Note: program subject to change. Workshop supported by NIH 9P41GM104601 "Center for Macromolecular Modeling and Bioinformatics".