B-spline tight frame based force matching method

JOURNAL OF COMPUTATIONAL PHYSICS

卷:362

Article

Yang, Jianbin^1,2  Zhu, Guanhua³  Tong, Dudu³  Lu, Lanyuan³  Shen, Zuowei² 

[1] Hohai Univ, Dept Math, Nanjing 211100, Jiangsu, Peoples R China

[2] Natl Univ Singapore, Dept Math, Singapore 117543, Singapore

[3] Nanyang Technol Univ, Sch Biol Sci, Singapore 637551, Singapore

关键词: Force matching;    Coarse-grained methods;    Wavelet tight frames;    l(1)- regularized least squares;   

DOI  :  10.1016/j.jcp.2018.02.024

来源: Elsevier

【 摘 要 】

In molecular dynamics simulations, compared with popular all-atom force field approaches, coarse-grained (CG) methods are frequently used for the rapid investigations of long time-and length-scale processes in many important biological and soft matter studies. The typical task in coarse-graining is to derive interaction force functions between different CG site types in terms of their distance, bond angle or dihedral angle. In this paper, an l(1)-regularized least squares model is applied to form the force functions, which makes additional use of the B-spline wavelet frame transform in order to preserve the important features of force functions. The B-spline tight frames system has a simple explicit expression which is useful for representing our force functions. Moreover, the redundancy of the system offers more resilience to the effects of noise and is useful in the case of lossy data. Numerical results for molecular systems involving pairwise non-bonded, three and four-body bonded interactions are obtained to demonstrate the effectiveness of our approach. (C) 2018 Elsevier Inc. All rights reserved.

【 授权许可】

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