Optimizing working parameters of the smooth particle mesh Ewald algorithm in terms of accuracy and efficiency

The Journal of Chemical Physics
Han WangChristian Holm

Abstract

We construct an accurate error estimate for the root mean square force error of the smooth particle mesh Ewald (SPME) algorithm, which is often used for molecular dynamics simulations, where charge configurations under periodic boundary conditions require considerable amounts of CPU time. The error estimates are provided for the ik- as well as analytical force differentiation schemes, and their validity is tested for a random homogeneous sample system. Finally, we demonstrate that it is possible to straightforwardly and precisely determine the SPME parameters via the error estimates prior to the simulation for a predetermined accuracy. This can save precious computer and user time and allows an easy choice of a suitable parameter set for nearly optimal speed.

Citations

Nov 12, 2013·Journal of Chemical Theory and Computation·Himanshu Paliwal, Michael R Shirts
Nov 13, 2012·Journal of Molecular Graphics & Modelling·Alireza SadeghifarAhmadreza F Ghobadi
Jul 23, 2013·Biophysical Journal·Rebecca J SwettAndrew L Feig
Jul 9, 2013·DNA Repair·Rebecca J SwettG Andrés Cisneros
Oct 3, 2014·The Journal of Chemical Physics·Jia LiuMyung-Hwan Whangbo
Apr 22, 2016·Interdisciplinary Sciences, Computational Life Sciences·Mubashir HassanSung-Yum Seo
Oct 30, 2016·Journal of Chemical Theory and Computation·Han WangJun Fang
Dec 24, 2016·International Journal of Molecular Sciences·Zaman AshrafSong Ja Kim
Mar 25, 2017·Chemical Biology & Drug Design·Phanikrishna ParchaBaskaran Rajasekaran
Aug 17, 2017·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Pervaiz Ali ChannarSung-Yum Seo
Apr 7, 2011·Journal of Computational Chemistry·Mark J Abraham, Jill E Gready
Mar 30, 2012·Faraday Discussions·Katharina WendlerLuigi Delle Site
Nov 7, 2012·Dalton Transactions : an International Journal of Inorganic Chemistry·Hongjun XiangMyung-Hwan Whangbo
Dec 25, 2012·Physical Chemistry Chemical Physics : PCCP·Florian Dommert, Christian Holm
Jul 19, 2019·Journal of Biomolecular Structure & Dynamics·Ludmila AricovDan-Florin Anghel
Mar 17, 2020·Journal of Biomolecular Structure & Dynamics·Khattab Al-Khafaji, Tugba Taskin Tok
Oct 2, 2017·The Journal of Chemical Physics·Han WangXingyu Gao
Apr 26, 2018·Nature Communications·Ahmad GebaiBhushan Nagar
Jul 16, 2017·Physical Review. E·Xingyu GaoHan Wang
Jun 19, 2018·Frontiers in Computational Neuroscience·Mubashir HassanAhmed A Moustafa
May 24, 2018·Neurological Sciences : Official Journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology·Mubashir HassanAhmed A Moustafa
Sep 26, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Han WangPingwen Zhang
Nov 18, 2020·Computational and Structural Biotechnology Journal·Masaud ShahHyun Goo Woo
Nov 19, 2020·Antibiotics·Jong H KimKirkwood M Land
Sep 26, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Claudio BertiClaudio Fiegna
Aug 29, 2013·Chemical Reviews·G Andrés CisnerosCeleste Sagui
Feb 19, 2016·Journal of Chemical Theory and Computation·Han Wang, Christof Schütte

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