Kastenholz Mika A, Hünenberger Philippe H
Laboratorium für Physikalische Chemie, ETH Zürich, CH-8093 Zürich, Switzerland.
J Chem Phys. 2006 Mar 28;124(12):124108. doi: 10.1063/1.2177249.
Artifacts induced by the application of periodic boundary conditions and lattice-sum methods in explicit-solvent simulations of (bio-)molecular systems are nowadays a major concern in the computer-simulation community. The present article reports a first step toward the design of a modified lattice-sum algorithm emulating nonperiodic boundary conditions, and therefore exempt of such periodicity-induced artifacts. This result is achieved here in the (more simple) context of continuum electrostatics. It is shown that an appropriate modification of the periodic Poisson equation and of its boundary conditions leads to a continuum-electrostatics scheme, which, although applied under periodic boundary conditions, exactly mimics the nonperiodic situation. The possible extension of this scheme to explicit-solvent simulations is outlined and its practical implementation will be described in more details in a forthcoming article.
在（生物）分子系统的显式溶剂模拟中，由周期性边界条件和晶格求和方法的应用所引起的伪影如今是计算机模拟领域的一个主要关注点。本文报道了朝着设计一种模拟非周期性边界条件的改进晶格求和算法迈出的第一步，因此该算法可避免此类周期性引起的伪影。此结果是在（更简单的）连续介质静电学背景下获得的。结果表明，对周期性泊松方程及其边界条件进行适当修改会得到一种连续介质静电学方案，该方案虽然在周期性边界条件下应用，但能精确模拟非周期性情况。概述了该方案向显式溶剂模拟扩展的可能性，其实际实现将在后续文章中更详细地描述。
