A different approach to dual-scale models

JOURNAL OF COMPUTATIONAL PHYSICS

卷:413

Article

Gowers, Richard J.^1,4  Carbone, Paola²  Di Pasquale, Nicodemo³ 

[1] Univ New Hampshire, Coll Engn & Phys Sci, Durham, NH 03824 USA

[2] Univ Manchester, Dept Chem Engn & Analyt Sci, Manchester M13 9PL, Lancs, England

[3] Univ Leicester, Sch Math & Actuarial Sci, Univ Rd, Leicester LE1 7RH, Leics, England

[4] NextMove Software Ltd, Innovat Ctr, Sci Pk,Milton Rd, Cambridge CB4 0EY, England

关键词: Molecular dynamics;    Coarse-graining;    Multi-scale modelling;   

DOI  :  10.1016/j.jcp.2020.109465

来源: Elsevier

【 摘 要 】

Dual-resolution models which combine atomistic and coarse-grained details are usually built sequentially. First, the coarse-grained model is optimized and subsequently atomistic regions are introduced. Finally, these two different resolutions are connected together. Here, we present a methodology for a direct construction of these dual-resolution models without the inclusion of these two stages. Our model takes advantage of the use of virtual sites and retain the full atomistic structure of the molecules by coarse-graining only some selected intermolecular interactions. The method is tested on different models of octanol where the atomistic details in the OH head groups are retained at an atomistic level, while an iterative Boltzmann inversion CG forcefield is used to model the alkyl tails. The procedure is applied to an All-Atom and United-Atom model. The dual-resolved version of each atomistic model is able to retain the hydrogen bonding structure and dynamics, with the united atom model showing slightly better results. Finally, the current computational performance of such a model is explored and compared against the potential theoretical performance. (C) 2020 Elsevier Inc. All rights reserved.

【 授权许可】

Free