Iterative Reconstruction of Memory Kernels

Journal of Chemical Theory and Computation
Gerhard JungFriederike Schmid

Abstract

In recent years, it has become increasingly popular to construct coarse-grained models with non-Markovian dynamics to account for an incomplete separation of time scales. One challenge of a systematic coarse-graining procedure is the extraction of the dynamical properties, namely, the memory kernel, from equilibrium all-atom simulations. In this article, we propose an iterative method for memory reconstruction from dynamical correlation functions. Compared to previously proposed noniterative techniques, it ensures by construction that the target correlation functions of the original fine-grained systems are reproduced accurately by the coarse-grained system, regardless of time step and discretization effects. Furthermore, we also propose a new numerical integrator for generalized Langevin equations that is significantly more accurate than the more commonly used generalization of the velocity Verlet integrator. We demonstrate the performance of the above-described methods using the example of backflow-induced memory in the Brownian diffusion of a single colloid. For this system, we are able to reconstruct realistic coarse-grained dynamics with time steps about 200 times larger than those used in the original molecular dynamics s...Continue Reading

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Citations

Sep 9, 2019·The European Physical Journal. E, Soft Matter·Julian KapplerRoland R Netz
Jan 16, 2020·Soft Matter·Lucas L Treffenstädt, Matthias Schmidt
Dec 10, 2017·The Journal of Chemical Physics·Hugues MeyerTanja Schilling
Feb 20, 2019·Physical Review. E·Nicodemo Di PasqualeMatteo Icardi
May 10, 2019·The Journal of Chemical Physics·Hugues MeyerTanja Schilling
May 9, 2019·Interface Focus·Ravinda S GunaratneRadek Erban
Feb 3, 2018·The Journal of Chemical Physics·Matthias Schmidt
Aug 3, 2018·The Journal of Chemical Physics·Yining HanGregory A Voth
Jan 3, 2019·The Journal of Chemical Physics·Gregor Deichmann, Nico F A van der Vegt
May 10, 2019·The Journal of Chemical Physics·Hee Sun LeeEric F Darve
Sep 25, 2017·The Journal of Chemical Physics·Julija Zavadlav, Matej Praprotnik
Apr 3, 2019·Physical Review. E·Pep EspañolD Duque-Zumajo
Oct 26, 2020·The European Physical Journal. E, Soft Matter·Bernhard G MitterwallnerRoland R Netz
Sep 22, 2020·Journal of Computational Physics·Francesca GroganNathan A Baker
Mar 1, 2021·The Journal of Chemical Physics·Yining HanGregory A Voth
Feb 20, 2021·Physical Review Letters·Lucas L Treffenstädt, Matthias Schmidt
Mar 11, 2021·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Bing LiFriederike Schmid
Feb 17, 2021·Journal of Physics. Condensed Matter : an Institute of Physics Journal·N BockiusM Hanke
May 14, 2021·The Journal of Physical Chemistry. B·Viktor KlippensteinNico F A van der Vegt
Jun 17, 2021·Soft Matter·Gerhard Jung, Friederike Schmid
Jul 10, 2021·The Journal of Chemical Physics·Viktor Klippenstein, Nico F A van der Vegt
Jul 31, 2021·Proceedings of the National Academy of Sciences of the United States of America·Cihan AyazRoland R Netz

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