反玻尔兹曼迭代多尺度分子动力学研究碳纳米管和氨基酸之间的相互作用。

Inverse Boltzmann Iterative Multi-Scale Molecular Dynamics Study between Carbon Nanotubes and Amino Acids.

机构信息

T-Life Research Center, State Key Laboratory of Surface Physics, Department of Physics, Fudan University, Shanghai 200433, China.

Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China.

出版信息

Molecules. 2022 Apr 27;27(9):2785. doi: 10.3390/molecules27092785.

DOI:10.3390/molecules27092785

PMID:35566140

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9104776/

Abstract

Our work uses Iterative Boltzmann Inversion (IBI) to study the coarse-grained interaction between 20 amino acids and the representative carbon nanotube CNT55L3. IBI is a multi-scale simulation method that has attracted the attention of many researchers in recent years. It can effectively modify the coarse-grained model derived from the Potential of Mean Force (PMF). IBI is based on the distribution result obtained by All-Atom molecular dynamics simulation; that is, the target distribution function and the PMF potential energy are extracted, and then, the initial potential energy extracted by the PMF is used to perform simulation iterations using IBI. Our research results have been through more than 100 iterations, and finally, the distribution obtained by coarse-grained molecular simulation (CGMD) can effectively overlap with the results of all-atom molecular dynamics simulation (AAMD). In addition, our work lays the foundation for the study of force fields for the simulation of the coarse-graining of super-large proteins and other important nanoparticles.

摘要

我们的工作使用迭代玻尔兹曼反演（IBI）来研究 20 种氨基酸与代表性碳纳米管 CNT55L3 之间的粗粒相互作用。IBI 是一种多尺度模拟方法，近年来引起了许多研究人员的关注。它可以有效地修改源自平均力势（PMF）的粗粒模型。IBI 基于全原子分子动力学模拟获得的分布结果；也就是说，提取目标分布函数和 PMF 位能，然后，使用 IBI 对 PMF 提取的初始位能进行模拟迭代。我们的研究结果已经经过了 100 多次迭代，最终，通过粗粒分子模拟（CGMD）获得的分布可以有效地与全原子分子动力学模拟（AAMD）的结果重叠。此外，我们的工作为模拟超大型蛋白质和其他重要纳米粒子粗粒化的力场研究奠定了基础。