Roles of boundary conditions in DNA simulations: analysis of ion distributions with the finite-difference Poisson-Boltzmann method.

ABSTRACT: The wide use of lattice-sum strategies in biomolecular simulations has raised many questions on potential artifacts in these strategies. One interesting question is the artifacts in the counterion distributions of highly charged systems. As one would anticipate, Coulombic interactions under the periodic boundary condition may deviate noticeably from those under the free boundary condition in the highly charged systems, significantly influencing their counterion distributions. On the other hand, the electrostatic screening due to water molecules and mobile ions may effectively damp the possible periodic distortions in Coulombic interactions. Therefore, the magnitude of periodicity-induced artifacts in counterion distributions is not straightforward to dissect without detailed analyses. In t

SUBMITTER: Ye X 

PROVIDER: S-EPMC2711334 | biostudies-literature | 2009 Jul

REPOSITORIES: biostudies-literature