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

Molecules

Xinwen Ou¹  Junyan Luo²  Wanying Huang³ 

[1] Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China;Department of Physics, Zhejiang University of Science and Technology, Hangzhou 310023, China;T-Life Research Center, State Key Laboratory of Surface Physics, Department of Physics, Fudan University, Shanghai 200433, China;

关键词: multi-scale molecular dynamics;    IBI;    CBNs;   

DOI  :  10.3390/molecules27092785

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown