Elastic bag model for molecular dynamics simulations of solvated systems: application to liquid water and solvated peptides.
Elastic bag model for molecular dynamics simulations of solvated systems: application to liquid water and solvated peptides.
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用于溶剂化系统分子动力学模拟的弹性袋模型：应用于液态水和溶剂化肽。
DOI：
10.1021/jp057532s
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发表时间：
2006
期刊：
影响因子：
--
通讯作者：
B. Berne
中科院分区：
文献类型：
--
作者：
Yuhui Li;Goran Krilov;B. Berne
本文建立了分子动力学的波动弹性边界（FEB）模型，并通过对液态氩气的模拟验证了该模型的有效性。在FEB模型中，使用由弹簧连接的粒子组成的柔性边界来限制溶剂化系统，从而消除了对周期性边界条件的需要。在本研究中，我们将该模型扩展到模拟散装水和溶剂化丙氨酸二肽。修正了边界势和边界粒子相互作用函数，以保持边界的结构完整性，防止溶质-溶剂体系通过边界泄漏。计算了液态水的结构和动力特性，并与常规周期边界条件模拟结果进行了比较。通过分析溶剂化丙氨酸二肽的构象居群分布，探讨了该模型在生物分子模拟中的适用性。在大多数情况下，我们发现这两种模拟方法之间存在显著的一致性。
The fluctuating elastic boundary (FEB) model for molecular dynamics has recently been developed and validated through simulations of liquid argon. In the FEB model, a flexible boundary which consists of particles connected by springs is used to confine the solvated system, thereby eliminating the need for periodic boundary conditions. In this study, we extend this model to the simulation of bulk water and solvated alanine dipeptide. Both the confining potential and boundary particle interaction functions are modified to preserve the structural integrity of the boundary and prevent the leakage of the solute-solvent system through the boundary. A broad spectrum of structural and dynamic properties of liquid water are computed and compared with those obtained from conventional periodic boundary condition simulations. The applicability of the model to biomolecular simulations is investigated through the analysis of conformational population distribution of solvated alanine dipeptide. In most cases we find remarkable agreement between the two simulation approaches.