Large-scale simulations of the ribosome: a new landmark in computational biology
KY Sanbonmatsu and CS Tung, SciDAC 2006: Scientific Discovery Through Advanced Computing, 46, 334-342 (2006).
Within computational biology, all-atom simulation is the most computationally demanding field, in terms of compute load, communication speed, and memory load. Here, we report molecular dynamics simulation results for the ribosome, using 2.64 x 10(6) atoms, the largest all-atom biomolecular simulation published to date. The ribosome is the largest asymmetric biological structure solved to date to atomic resolution (2.8 angstrom). While simulations requiring long-range electrostatic forces have been previously restricted to much smaller systems, breakthroughs in electrostatic force calculation and dynamic load balancing have enabled molecular dynamics simulations of large biomolecular complexes. The LANL Q Machine played a key role in enabling such large simulations to be performed. The LANL Q machine displays approximately 85% parallel scaling efficiency for the ribosome system on 1024 CPUs. Using the targeted molecular dynamics algorithm, we have simulated the rate- limiting step in genetic decoding by the ribosome. The simulations use experimentally determined ribosome structures in different functional states as the initial and final conditions, making our simulations entirely and rigorously consistent with these experimental data. The simulations have identified candidate 23S rRNA nucleotides important for the accommodation of tRNA into the ribosome during protein synthesis.
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