Analysis of the function of a large-scale supra-biomolecule system by molecular dynamics simulation system, SCUBA. Simulation codes for hUge biomolecular assembly (Annual Report of the Earth Simulator Center, 2006 issue)

The Earth Simulator has the highest power ever achieved to perform molecular dynamics simulation of large-scale supra-molecular systems. We are developing a molecular dynamics simulation system, called SCUBA, which is designed to run a system composed of more than a million particles efficiently on parallel computers. This fiscal year, the arrays used in the program of SCUBA were intensively optimized to reduce the amount of memory use. This optimization enabled SCUBA to perform molecular dynamics simulations of large-scale supra-molecular systems comprised of more than a million atoms on the Earth Simulator. Moreover, the Martyna-Klein-Tuckerman algorithm was extended to utilize the multiple time step method, which increases the time step length significantly. Then, in order to elucidate the dynamics of the 70S ribosome, molecular dynamics simulation of the 70S ribosome including its explicit solvent, a system which is composed of about two million atoms, has been performed using SCUBA. A model of a nascent polypeptide was included in the system to investigate how the nascent polypeptide passes through the exit tunnel within the large subunit of the 70S ribosome. The ratchet-like motion of the 70S ribosome, which is thought to be important for the genetic translation, was successfully observed. (author)