SC2006 Talks and Demonstrations

When: November 13-16 2006

Support: NAMD, VMD, and BioCoRE are developed by the Theoretical and Computational Biophysics Group at the Beckman Institute of the University of Illinois, supported by the NIH National Center for Research Resources and the National Science Foundation.


NIH National Center for Research Resources Booth Presentations

Title: Exploring Biomolecular Machines with Supercomputers
Location: University of San Diego NBCR booth (#439, aisle between Microsoft and NEC, next to Penguin Computing)
Full Information:
Times: Monday 8-9pm
Presenters: James Phillips
Contributors: John Stone, Kirby Vandivort, Robert Brunner
Contacts: Peter Arzberger at SDSC
TCBG Support: Prepare and present demo.

The Theoretical and Computational Biophysics Group (TCBG), an NIH Resource for Macromolecular Modeling and Bioinformatics, is located at the Beckman Institute of the University of Illinois at Urbana-Champaign (UIUC). The Resource brings advanced molecular modeling, bioinformatics, and computational technologies to bear on questions of biomedical relevance through direct collaboration with experimental researchers, the distribution of user-friendly cutting-edge software, and a broad range of training and dissemination activities.

The flagship TCBG software packages NAMD, VMD, and BioCoRE, all distributed free of charge with source code, facilitate the discovery process from analysis, through modeling, to visualization of the molecular apparatus in biological cells:

  • NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code used regularly to simulate systems of 300,000 atoms and beyond on both large supercomputers and inexpensive Linux clusters.
  • VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using hardware-accelerated 3-D graphics and built-in scripting.
  • BioCoRE is a collaborative work environment that allows biomedical researchers to visualize information, to share resources, and to interact with each other and with research tools via a common infrastructure and across distance.


For improved VMD performance on the tiled display use "display cachemode on"; this is primarily useful for rotating static structures.