Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions:: a continuum electrostatics study
Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions:: a continuum electrostatics study
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DOI：
10.1016/s0301-4622(99)00007-1
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发表时间：
1999-04-05
影响因子：
3.8
通讯作者：
McCammon, JA
中科院分区：
文献类型：
--
作者：
Hünenberger, PH;McCammon, JA
埃瓦尔德和相关的方法现在经常用于显式溶剂模拟的生物分子，虽然他们强加了一个人工的周期性系统，本质上是非周期性的。这种近似的后果应进行评估，因为它们可能会严重影响埃瓦尔德边界条件下的计算机模拟的可靠性。在本研究中，我们使用一种基于连续静电的方法来研究生物分子中构象平衡的平均力的电势上可能的生物性诱导的伪影的性质和幅度。三个模型系统和途径被认为是：聚丙氨酸寡肽（展开），DNA四核苷酸（分离的链），和蛋白质Sac 7 d（构象从分子动力学模拟）。人工周期性可能会显着影响这些构象平衡，在每种情况下稳定的生物分子的最紧凑的构象。三个因素增强结晶度引起的伪影：（i）低介电常数的溶剂;（ii）与晶胞的尺寸相比不可忽略的溶质尺寸;以及（iii）非中性溶质。无论是中性的溶质，也没有电荷对的距离超过一半的边缘的单位电池不保证不存在的文物。(C)1999 Elsevier Science B. V.保留所有权利。
Ewald and related methods are nowadays routinely used in explicit-solvent simulations of biomolecules, although they impose an artificial periodicity in systems which are inherently non-periodic. The consequences of this approximation should be assessed, since they may crucially affect the reliability of computer simulations under Ewald boundary conditions. In the present study we use a method based on continuum electrostatics to investigate the nature and magnitude of possible periodicity-induced artifacts on the potentials of mean force for conformational equilibria in biomolecules. Three model systems and pathways are considered: polyalanine oligopeptides (unfolding), a DNA tetranucleotide (separation of the strands), and the protein Sac7d (conformations from a molecular dynamics simulation). Artificial periodicity may significantly affect these conformational equilibria, in each case stabilizing the most compact conformation of the biomolecule. Three factors enhance periodicity-induced artifacts: (i) a solvent of low dielectric permittivity; (ii) a solute size which is non-negligible compared to the size of the unit cell; and (iii) a non-neutral solute. Neither the neutrality of the solute nor the absence of charge pairs at distances exceeding half the edge of the unit cell do guarantee the absence of artifacts. (C) 1999 Elsevier Science B.V. All rights reserved.