High performance computing in biology: multimillion atom simulations of nanoscale systems.

ABSTRACT: Computational methods have been used in biology for sequence analysis (bioinformatics), all-atom simulation (molecular dynamics and quantum calculations), and more recently for modeling biological networks (systems biology). Of these three techniques, all-atom simulation is currently the most computationally demanding, in terms of compute load, communication speed, and memory load. Breakthroughs in electrostatic force calculation and dynamic load balancing have enabled molecular dynamics simulations of large biomolecular complexes. Here, we report simulation results for the ribosome, using approximately 2.64 million atoms, the largest all-atom biomolecular simulation published to date. Several other nano-scale systems with different numbers of atoms were studied to measure the performance

SUBMITTER: Sanbonmatsu KY 

PROVIDER: S-EPMC1868470 | biostudies-literature | 2007 Mar

REPOSITORIES: biostudies-literature