| Effectiveness of coarse graining degree and speedup on the dynamic properties of homopolymer | |
Liao LJ(廖丽涓)1 ; Meng CY(孟昶宇)1,2; Huang CG(黄晨光)1,2
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| Corresponding Author | Liao, Lijuan([email protected]) |
| Source Publication | JOURNAL OF MOLECULAR MODELING
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| 2021-01-28 | |
| Volume | 27Issue:2Pages:9 |
| ISSN | 1610-2940 |
| Abstract | 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. |
| Keyword | Coarse graining (CG) degree Speedup Iterative Boltzmann inversion (IBI) Temperature transferability Dynamic behavior |
| DOI | 10.1007/s00894-020-04661-5 |
| Indexed By | SCI |
| Language | 英语 |
| WOS ID | WOS:000616165400003 |
| WOS Research Area | Biochemistry & Molecular Biology ; Biophysics ; Chemistry ; Computer Science |
| WOS Subject | Biochemistry & Molecular Biology ; Biophysics ; Chemistry, Multidisciplinary ; Computer Science, Interdisciplinary Applications |
| Funding Project | National Natural Science Foundation of China[11672314] |
| Funding Organization | National Natural Science Foundation of China |
| Classification | Q3 |
| Ranking | 1 |
| Contributor | Liao, Lijuan |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://dspace.imech.ac.cn/handle/311007/86101 |
| Collection | 流固耦合系统力学重点实验室 |
| Affiliation | 1.Chinese Acad Sci, Inst Mech, Key Lab Mech Fluid Solid Coupling Syst, 15,Beisihuan West Rd, Beijing 100190, Peoples R China; 2.Univ Chinese Acad Sci, Sch Engn Sci, 19 A,Yuquan Rd, Beijing 100049, Peoples R China |
| Recommended Citation 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.Rp_Au:Liao, Lijuan |
| 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. |
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| Jp2021075.pdf（2167KB） | 期刊论文 | 出版稿 | 开放获取 | CC BY-NC-SA | View Download | |
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