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混合粒子-场分子动力学方法:生物膜高效粗粒模型的途径。

A hybrid particle-field molecular dynamics approach: a route toward efficient coarse-grained models for biomembranes.

机构信息

Dipartimento di Chimica e Biologia, Università di Salerno, I-84084 SA, Italy.

出版信息

Phys Biol. 2013 Aug;10(4):045007. doi: 10.1088/1478-3975/10/4/045007. Epub 2013 Aug 2.

Abstract

This paper gives an overview of the coarse-grained models of phospholipids recently developed by the authors in the frame of a hybrid particle-field molecular dynamics technique. This technique employs a special class of coarse-grained models that are gaining popularity because they allow simulations of large scale systems and, at the same time, they provide sufficiently detailed chemistry for the mapping scheme adopted. The comparison of the computational costs of our approach with standard molecular dynamics simulations is a function of the system size and the number of processors employed in the parallel calculations. Due to the low amount of data exchange, the larger the number of processors, the better are the performances of the hybrid particle-field models. This feature makes these models very promising ones in the exploration of several problems in biophysics.

摘要

本文概述了作者最近在混合粒子-场分子动力学技术框架下开发的磷脂粗粒度模型。该技术采用了一类特殊的粗粒度模型,由于它们允许对大规模系统进行模拟,同时为所采用的映射方案提供了足够详细的化学信息,因此这些模型越来越受欢迎。我们的方法与标准分子动力学模拟的计算成本比较是系统大小和并行计算中使用的处理器数量的函数。由于数据交换量低,处理器数量越多,混合粒子-场模型的性能越好。这个特性使得这些模型在探索生物物理学中的几个问题方面非常有前途。

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