Based On The Substructure Synthesis Method Of Biological Macromolecular Structure Of Whole Atom Simulation Calculation

There are increasing interests in the dynamics and functions of very large bio-structures, including ribosome. F1-ATPase. actin-filaments, virus, membrane systems, etc. However, dynamic simulations of very large bio-structures are challenging due to the requirement of huge memory and cpu time. In this paper, based on previous work [28] on substructure synthesis method (SSM) for simulating very large complexes, we introduced a new type of geometry-compatible conditions and derived an all-atom based SSM scheme which can be easily applied to very large bio-structures of various types of substructure interactions. We applied this method to simulating all-atom dynamics of a 13mer F-actin filament with and without ATP/ADP bindings. We found the dynamics of the overall filament depends, in a cer-tain manner, on the binding nucleotide ligands. We also compared our re-sults with all-atom CHARMM simulations for relatively small structures, and found that our calculations are reliable.