Molecular Dynamics Simulation System for Structural Analysis of Biomolecules by High Performance Computing

We have developed an integrated molecular simulation system for biological macromolecules, called SCUBA (Simulation Codes for hUge Biomolecular Assembly) which is designed to run a biomolecule system composed of more than one million particles efficiently on parallel computers. SCUBA is now being used not only for molecular dynamics (MD) simulations but also to determine the 3D structure of supra-macromolecules. For the latter purpose, a new method to fit a high-resolution X-ray structure at a certain reaction state into low-resolution electron microscopy (EM) data at different reaction states has been developed. In our method, the fitting is carried out using MD simulations in explicit water medium; the target function considers restraints to fit the X-ray structure into an EM density map, and the all-atom interactions for all the molecules including the water medium. This method was implemented into SCUBA and applied to ribosome, one of the supra-biomolecules utilized for translating genetic information to the amino acid sequence. The system was composed of more than 2 million atoms. The method showed that SCUBA can carry out the fitting simulation with a high parallelization efficiency ratio of more than 50% using 512 CPU cores of PRIMERGY BX900 supercomputer at the Japan Atomic Energy Agency.