Using internal and collective variables in Monte Carlo simulations of nucleic acid structures: chain breakage/closure algorithm and associated Jacobians.

摘要: This article describes a method for solving the geometric closure problem simplified models of nucleic acid structures by using constant bond lengths approximation. The resulting chain breakage/closure equations, formulated in space variable torsion and angles, are easy to solve, have only two solutions. analytical simplicity is contrast with high complexity angle at most 16 solutions, which has been dealt several authors was solved analytically Wu Deem (J. Chem. Phys. 1999, 111, 6625). discussion on choice variables associated Jacobians focussed question how conformational equilibration affected Monte Carlo simulations molecular systems. In addition phosphate backbone, it necessary also solve five-membered flexible furanose sugar ring. Explicit equations given both complete four-variable model ring phase-amplitude ring, based approximate two-variable introduced Gabb et al. Comput. 1995, 16, 667). suggested algorithm can be combined collective defined translations rotations monomeric nucleotide units. comparison simple internal coordinate moves, concerted moves describe local structural changes that acceptance rates enable fast equilibration. Appropriate put forward prospective acids, but easily adapted other biomolecular systems, such as proteins lipid biological membranes.