NAMD/VMD-based SPICE wins the HPC Analytics Challenge Award at SC|05

 

SC2005 Talks and Demonstrations

When: November 12-18 2005

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.

URL: http://sc05.supercomputing.org/

NIH National Center for Research Resources Booth Presentations

Title: Exploring Biomolecular Machines with Supercomputers
Location: NBCR (NCRR) booth (#656, level 4, far north end, near hotel tower)
Full Information: http://nbcr.net/events/supercomputing/2005/
Times: Monday 8-9pm, Tuesday 10am-2pm, Wednesday 10am-2pm & 4-6pm
Presenters: Jordi Cohen and James Phillips
Contributors: John Stone, Kirby Vandivort, Robert Brunner, Marcos Sotomayor
Contacts: Peter Arzberger at SDSC
TCBG Support: Prepare and present demo.
Abstract:

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.
The simulations of gas transport in proteins (shown below) highlighted in this presentation will demonstrate how this NIH-supported, freely available software is opening a new era in computational biology.

Notes:

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

NCSA and TeraGrid Booth Presentations

Title: Grid-Based NAMD Simulation of Gas Transport in Proteins
Location: NCSA booth (#1639, level 4, far south end, near Dell booth)
                  TeraGrid booth (#662, level 4, far north end, near hotel tower)
Full Information: http://www.ncsa.uiuc.edu/Conferences/SC2005/
Time: Monday 7-8pm at NCSA, Tuesday 12-1pm at TeraGrid
Presenters: Jordi Cohen and James Phillips
Contributors: John Stone, Kirby Vandivort, Robert Brunner, Marcos Sotomayor
Collaborators: Dynome Project (http://www.dynome.org/) demo in UK e-Science booth (#922)
Contacts: Karen Green at NCSA
TCBG Support: Prepare and present demo.
Abstract:

Researchers at the Theoretical and Computational Biophysics Group at the University of Illinois (TCBG) are now able to image gas transport pathways inside proteins, which has many implications for biotechnology and science. For this research, a large number of simulations need to be run and monitored, and the traditional means of doing so is very wasteful of the researchers' time. To solve this problem, a grid submission engine (NAMD-G) targeted towards biomolecular simulations running the NAMD software, has been developed by NCSA in collaboration with TCBG personnel. From the researchers' host machines, NAMD-G can farm out a large number of jobs, in parallel, to the Linux clusters at NCSA and to other supercomputers on the TeraGrid. In addition, NAMD-G monitors and manages multiple sequences of linked simulation jobs, and performs the necessary transfers and backups on all of their associated files on an as-needed basis. During this presentation, the scientific backround of the gas transport process, the NIH-supported, freely available (at www.ks.uiuc.edu) NAMD and VMD software, and the NAMD-G submission engine running live, will all be showcased.