title: A further implementation of the rotational symmetry boundary conditions for calculations of P4(3)2(1)2 symmetry crystals.
abstract: One of the most accurate styles of protein simulation is to calculate proteins in crystalline environment without neglect of long-range interactions. The long-range interactions can be accelerated by various methods. However, as a unit cell of a protein crystal is a large molecular assembly, its simulation is still unpractical without high-speed computers. Thus this article is addressed to the reduction of calculational volumes for protein crystal simulation by a further implementation of the rotational symmetry boundary condition method. For protein crystals in P4(3)2(1)2 symmetry, a computational cell and related tables were developed. A 120-ps molecular dynamics simulation was performed for a P4(3)2(1)2 symmetry crystal of glycogen phosphorylase b under rotational symmetry boundary conditions. The computational cell was one-eighth of the unit cell in volume, and less than about one-fourth of the conventional periodic boundary box. Generation of neighbor atom pair lists was greatly accelerated, and thus the simulation was practical even with a personal computer.
authors.affiliation: School of Science, Kitasato University, Kanagawa-Ken, Japan.
authors.forename: S
authors.initials: S
authors.lastname: Yoneda
mesh_terms: D003198:Computer Simulation; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D010763:Phosphorylase b / Q000737:chemistry*
chemical_list: D010763:Phosphorylase b