Department of Chemistry and Biochemistry and of Physics, University of California, Santa Barbara, Santa Barbara, California 93106, United States.
J Phys Chem B. 2012 Jul 26;116(29):8337-49. doi: 10.1021/jp2097263. Epub 2012 Mar 2.
Many problems of interest in modern science originate from the complex network of interactions of different molecular structures, each possessing its own typical length and time scale of relevance. In such materials, nontrivial properties emerge from the different length and time scales involved that could not be predicted from the properties of each individual subunit taken alone. A solution to the formidable theoretical and computational issues raised by these systems involves coarse-graining, a procedure in which multiple atoms are grouped into a few interaction sites. The coarse-grained approach aims at constructing an effective Hamiltonian from available information about the system and then using this Hamiltonian to investigate the behavior of the system on the length and time scales of interest. In this paper, we aim at determining how far we can coarse-grain a system using only the commonly used pairwise, spherically symmetric potentials, as well as assessing the impact of poor initial sampling on the quality of the resulting coarse-grained model. Coarse-graining is performed following the multiscale coarse-graining (MS-CG) methodology, and we use as a model system the N-methylacetamide (NMA) molecule, a simple representation of a peptide bond, which can adopt two conformations, cis and trans. Our simulations reveal that as the coarse-graining becomes more aggressive multibody effects start to emerge and that the initial sampling of conformations can adversely bias the model in the case of heavy coarse-graining.
许多现代科学感兴趣的问题源于不同分子结构之间复杂的相互作用网络，每个分子结构都具有自己典型的相关长度和时间尺度。在这些材料中，从单独考虑每个单个亚基的性质无法预测的不同长度和时间尺度中出现了重要性质。解决这些系统提出的艰巨的理论和计算问题的一种方法涉及粗粒化，这是一种将多个原子分组为少数相互作用位点的过程。粗粒化方法旨在从系统的可用信息构建有效哈密顿量，然后使用该哈密顿量研究系统在感兴趣的长度和时间尺度上的行为。在本文中，我们旨在确定仅使用常用的成对、球对称势，我们可以在多大程度上对系统进行粗粒化，并评估初始采样不良对生成的粗粒化模型质量的影响。粗粒化是按照多尺度粗粒化 (MS-CG) 方法进行的，我们使用 N-甲基乙酰胺 (NMA) 分子作为模型系统，NMA 是肽键的简单表示，它可以采取顺式和反式两种构象。我们的模拟表明，随着粗粒化变得更加激进，多体效应开始出现，并且在重粗粒化的情况下，构象的初始采样可能会使模型产生偏差。
