Glutamate Receptor Molecular Dynamics Simulation
Molecular dynamics simulation of protein

The protein NNDA is a glutamate receptor in the human brain and is associated with memory and learning. Researchers study it because both drugs and toxicants bind to it, making it an important drug target. LLNL scientists use computational modeling to study how small molecules interact with this and related proteins to identify important binding residues and molecule-induced dynamic changes. This atomistic molecular dynamics simulation—the largest protein system that Livermore biologists model, with about one million atoms—shows an ion channel that allows cations to flow through. It is composed of four proteins and sits within the cellular membrane. For more information, visit the Biochemical and Biophysical Systems Group website.

Code: NAMD
Machine: Vulcan
Processors: 8,192 (512 nodes at 16 processors per node)
Run time: approximately 48 hrs, so approximately 400,000 CPU hours
Researchers: Tim Carpenter, Felice Lightstone