Resource for Macromolecular Modeling and Bioinformatics

Resource for Macromolecular Modeling and Bioinformatics

Research Emphasis

The resource studies large biomolecular processes in living cells, focusing on membrane proteins that mediate the exchange of materials and information across, in particular, biological membranes as well as the conversion between electro-osmotic, mechanical, and chemical energy. It also develops software for large-scale simulations. Software tools include nanoscale molecular dynamics (NAMD), a molecular dynamics simulation program used for classic, atomistic molecular dynamics simulations of large biomolecular aggregates; visual molecular dynamics (VMD), a molecular visualization program for displaying, animating, and analyzing both large and small biomolecular systems using three-dimensional (3-D) graphics and built-in scripting; BioCoRE, a Web-based, tool-oriented collaboratory for biomedical research and training.

Current Research

Current research includes interactive molecular dynamics (IMD) for the manipulation of molecular simulations with real-time force feedback and interactive display; investigations of aquaporin channels, mechanosensitive channel, ATP synthase, chloride channel, photosynthetic proteins, visual receptors, and proteins with mechanical functions; efficient evaluation of force fields and integration schemes for simulation of very large biomolecular systems; efficient distributed molecular dynamics programs on workstation clusters and massively parallel machines; and the continued development of NAMD, VMD, and BioCoRE.

Resource Capabilities

Instruments

Three main computational platforms are in use: 100 Athlon PC nodes running as four Scyld Beowulf Linux clusters, the primary development platform for the group's molecular dynamics program, NAMD; four Microway Alpha AXP21264-500 dual-processor nodes, two with 4 gigabytes (GB) of memory, primarily used for large-memory jobs such as quantum simulations; and two dual-processor SunBlade 2000 systems with XVR1000 video cards and 4 GB of memory, used for both visualization and large memory jobs. These systems are controlled using a shared queuing system. Four Sun Enterprise 250 servers with a combined total of 2.75 terabytes of disk space serve the network-wide home and project directories. The servers are backed up daily on four DLT4000 tape changers. The key graphics platforms include the aforementioned SunBlade 2000 systems; one Sun Ultra 80 and one Ultra 60 system, each with Expert 3-D graphics; and an eight-processor SGI Onyx2 with InfiniteReality graphics. Nearly all researcher workstations are equipped with 3-D video cards and are capable of real-time stereoscopic visualization. The Sun Ultra 80 drives a stereo-capable Electrohome Marquee 8500LC projector in the resource's 3-D projection facility.

Special Features

Special features include IMD; VMD, a visualization program for interactive display and animation of molecules; NAMD, a parallel message-driven molecular dynamics program reaching teraflop performance; and BioCoRE, an integrated set of computational tools that function as an interactive visual computing environment for the simulation and collaborative study of biopolymers over distance and as a training platform.