Effectiveness of coarse graining degree and speedup on the dynamic properties of homopolymer
文献类型：期刊论文
| 作者 | Liao LJ(廖丽涓)2 ; Meng CY(孟昶宇)1,2; Huang CG(黄晨光)1,2
|
| 刊名 | JOURNAL OF MOLECULAR MODELING
 |
| 出版日期 | 2021-01-28 |
| 卷号 | 27期号:2页码:9 |
| 关键词 | Coarse graining (CG) degree Speedup Iterative Boltzmann inversion (IBI) Temperature transferability Dynamic behavior |
| ISSN号 | 1610-2940 |
| DOI | 10.1007/s00894-020-04661-5 |
| 通讯作者 | Liao, Lijuan(liaohuanxin@hotmail.com) |
| 英文摘要 | Evaluation of effective coarse graining (CG) degree and reasonable speedup relative to all-atomistic (AA) model was conducted to provide a basis for building appropriate larger-scale model. The reproducibility of atomistic conformation and temperature transferability both act as the analysis criteria to resolve the maximum acceptable CG degree. Taking short- and long time spans into account simultaneously in the estimation of computational speedup, a dynamic scaling factor is accessible in fitting mean squared displacement ratio of CG to AA as an exponential function. Computing loss in parallel running is an indispensable component in acceleration, which was also added in the evaluation. Subsequently, a quantified prediction of CG speedup arises as a multiplication of dynamic scaling factor, computing loss, time step, and the square of reduction in the number of degrees of freedom. Polyethylene oxide was adopted as a reference system to execute the direct Boltzmann inversion and iterative Boltzmann inversion. Bonded and non-bonded potentials were calculated in CG models with 1 similar to 4 monomers per bead. The effective CG degree was determined as two at the most with a speedup of four orders magnitude over AA in this study. Determination of effectiveness CG degree and the corresponding speedup prediction provide available tools in larger spatiotemporal-scale calculations. |
| 分类号 | Q3 |
| 资助项目 | National Natural Science Foundation of China[11672314] |
| WOS研究方向 | Biochemistry & Molecular Biology ; Biophysics ; Chemistry ; Computer Science |
| 语种 | 英语 |
| WOS记录号 | WOS:000616165400003 |
| 资助机构 | National Natural Science Foundation of China |
| 其他责任者 | Liao, Lijuan |
| 源URL | [http://dspace.imech.ac.cn/handle/311007/86100]  |
| 专题 | 力学研究所_流固耦合系统力学重点实验室(2012-) |
| 作者单位 | 1.Univ Chinese Acad Sci, Sch Engn Sci, 19 A,Yuquan Rd, Beijing 100049, Peoples R China 2.Chinese Acad Sci, Inst Mech, Key Lab Mech Fluid Solid Coupling Syst, 15,Beisihuan West Rd, Beijing 100190, Peoples R China; |
| 推荐引用方式 GB/T 7714 | Liao LJ,Meng CY,Huang CG. Effectiveness of coarse graining degree and speedup on the dynamic properties of homopolymer[J]. JOURNAL OF MOLECULAR MODELING,2021,27(2):9. |
| APA | 廖丽涓,孟昶宇,&黄晨光.(2021).Effectiveness of coarse graining degree and speedup on the dynamic properties of homopolymer.JOURNAL OF MOLECULAR MODELING,27(2),9. |
| MLA | 廖丽涓,et al."Effectiveness of coarse graining degree and speedup on the dynamic properties of homopolymer".JOURNAL OF MOLECULAR MODELING 27.2(2021):9. |
入库方式： OAI收割
来源：力学研究所
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