Fast and scalable evaluation of pairwise potentials

Hughey, S.; Alsnayyan, A. M. A.; Aktulga, Hasan Metin; Gao, Tong; Shanker, B.

doi:10.1016/j.cpc.2020.107248

Cited by 1 publication

(2 citation statements)

References 29 publications

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Section: Introductionmentioning

confidence: 99%

“…Accelerating reactive MD simulations can facilitate observation of these reactions within a reasonable simulation time. In this regard, there have been efforts such as developing custom algorithms to efficiently utilize the latest GPU hardware 12,33,34 and introducing probability space to dynamical simulations. 35−37 Non-reactive force fields often use a fixed bond scheme approach to improve computational efficiency by calculating bonded interactions over a predetermined neighbor list.…”

Section: ■ Introductionmentioning

confidence: 99%

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Machine Learning-Assisted Hybrid ReaxFF Simulations

Yılmaz

Woodward

Duin

2021

J. Chem. Theory Comput.

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We have developed a machine learning (ML)-assisted Hybrid ReaxFF simulation method (“Hybrid/Reax”), which alternates reactive and non-reactive molecular dynamics simulations with the assistance of ML models to simulate phenomena that require longer time scales and/or larger systems than are typically accessible to ReaxFF. Hybrid/Reax uses a specialized tracking tool during the reactive simulations to further accelerate chemical reactions. Non-reactive simulations are used to equilibrate the system after the reactive simulation stage. ML models are used between reactive and non-reactive stages to predict non-reactive force field parameters of the system based on the updated bond topology. Hybrid/Reax simulation cycles can be continued until the desired chemical reactions are observed. As a case study, this method was used to study the cross-linking of a polyethylene (PE) matrix analogue (decane) with the cross-linking agent dicumyl peroxide (DCP). We were able to run relatively long simulations [>20 million molecular dynamics (MD) steps] on a small test system (4660 atoms) to simulate cross-linking reactions of PE in the presence of DCP. Starting with 80 PE molecules, more than half of them cross-linked by the end of the Hybrid/Reax cycles on a single Xeon processor in under 48 h. This simulation would take approximately 1 month if run with pure ReaxFF MD on the same machine.

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