Low-Cost Linux Clusters for Biomolecular Simulations Using NAMD



  • Jim Phillips
  • Tim Skirvin
  • John Stone


  • Phillip Svinarski


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