NAMD Linux Cluster Tutorial 2001
Low-Cost Linux Clusters for Biomolecular Simulations Using NAMD
NCSA SiteInstructors
- Jim Phillips
- Tim Skirvin
- John Stone
Assistant
- Phillip Svinarski
Agenda
cover page
| 1:00pm | Designing a cluster for a small research group (PDF presentation) (3169) |
| 2:15pm | Hands-on: Building small Scyld clusters (instructions) (3169) |
| 3:15pm | Break (3151) |
| 3:30pm | Discussion: Cluster-building experiences (3414) |
| 3:45pm | Overview of NAMD and molecular dynamics (PDF presentation) (3414) |
| 4:00pm | Hands-on: Cluster performance experiments (instructions) (3414) |
| 4:45pm | Discussion: Cluster performance (3414) |
| 5:00pm | Adjourn |
| 5:15pm | Optional demo: Interactive MD and haptic device (3151) |
Recommended Readings
Scyld Beowulf Support Documentation (online)NAMD User's Guide (online or 4.5M PDF)
NAMD Release Notes (online)
Laxmikant Kalé, Robert Skeel, Milind Bhandarkar, Robert Brunner, Attila Gursoy, Neal Krawetz, James Phillips, Aritomo Shinozaki, Krishnan Varadarajan, and Klaus Schulten. NAMD2: Greater scalability for parallel molecular dynamics. Journal of Computational Physics, 151:283-312, 1999. abstract
