Low-Cost Linux Clusters for Biomolecular Simulations Using NAMD


Jim Phillips, John Stone, Tim Skirvin

NIH Resource for Macromolecular Modeling and Bioinformatics
Theoretical Biophysics Group, Beckman Institute, University of Illinois


1:00pm Designing a cluster for a small research group (3169)
2:15pm Hands-on: Building small Scyld clusters (3169)
3:15pm Break (3151)
3:30pm Discussion: Cluster-building experiences (3414)
3:45pm Overview of NAMD and molecular dynamics (3414)
4:00pm Hands-on: Cluster performance experiments (3414)
4:45pm Discussion: Cluster performance (3414)
5:00pm Adjourn
5:15pm Optional demo: Interactive MD and haptic device (3151)

Reference Web Sites

Scyld Beowulf: http://www.scyld.com/page/support/docs/

NAMD: http://www.ks.uiuc.edu/Research/namd/

TBG Clusters: http://www.ks.uiuc.edu/Development/Computers/beowulf.html