Assessing numerical methods for molecular and particle simulation

Soft Matter
Xiaocheng ShangBenedict Leimkuhler

Abstract

We discuss the design of state-of-the-art numerical methods for molecular dynamics, focusing on the demands of soft matter simulation, where the purposes include sampling and dynamics calculations both in and out of equilibrium. We discuss the characteristics of different algorithms, including their essential conservation properties, the convergence of averages, and the accuracy of numerical discretizations. Formulations of the equations of motion which are suited to both equilibrium and nonequilibrium simulation include Langevin dynamics, dissipative particle dynamics (DPD), and the more recently proposed "pairwise adaptive Langevin" (PAdL) method, which, like DPD but unlike Langevin dynamics, conserves momentum and better matches the relaxation rate of orientational degrees of freedom. PAdL is easy to code and suitable for a variety of problems in nonequilibrium soft matter modeling; our simulations of polymer melts indicate that this method can also provide dramatic improvements in computational efficiency. Moreover we show that PAdL gives excellent control of the relaxation rate to equilibrium. In the nonequilibrium setting, we further demonstrate that while PAdL allows the recovery of accurate shear viscosities at higher s...Continue Reading

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Citations

Mar 24, 2020·Proceedings. Mathematical, Physical, and Engineering Sciences·Xiaocheng Shang, Hans Christian Öttinger
Jan 17, 2019·The Journal of Chemical Physics·José Ruiz-FrancoEmanuela Zaccarelli
Jun 30, 2018·The European Physical Journal. E, Soft Matter·José Ruiz-FrancoEmanuela Zaccarelli
Feb 15, 2019·Entropy·Xiaobin DaiLi-Tang Yan

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Methods Mentioned

BETA
protein folding

Software Mentioned

LEBC
PAdL
BAOAB
LAMMPS
MATLAB

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