PMID: 9524932Aug 1, 1997Paper

A further implementation of the rotational symmetry boundary conditions for calculations of P4(3)2(1)2 symmetry crystals

Journal of Molecular Graphics & Modelling
S Yoneda

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.

References

May 25, 1977·Journal of Molecular Biology·F C BernsteinM Tasumi
Mar 5, 1991·Journal of Molecular Biology·D BarfordL N Johnson
Sep 1, 1995·Trends in Biochemical Sciences·R A Sayle, E J Milner-White
Aug 30, 1994·Proceedings of the National Academy of Sciences of the United States of America·D M YorkT A Darden
Oct 1, 1993·Proceedings of the National Academy of Sciences of the United States of America·D H KitsonA T Hagler

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