Machine learning prediction of interaction energies in rigid water clusters

Physical Chemistry Chemical Physics : PCCP
Samik BoseDebashree Ghosh

Abstract

Classical force fields form a computationally efficient avenue for calculating the energetics of large systems. However, due to the constraints of the underlying analytical form, it is sometimes not accurate enough. Quantum mechanical (QM) methods, although accurate, are computationally prohibitive for large systems. In order to circumvent the bottle-neck of interaction energy estimation of large systems, data driven approaches based on machine learning (ML) have been employed in recent years. In most of these studies, the method of choice is artificial neural networks (ANN). In this work, we have shown an alternative ML method, support vector regression (SVR), that provides comparable accuracy with better computational efficiency. We have further used many body expansion (MBE) along with SVR to predict interaction energies in water clusters (decamers). In the case of dimer and trimer interaction energies, the root mean square errors (RMSEs) of the SVR based scheme are 0.12 kcal mol-1 and 0.34 kcal mol-1, respectively. We show that the SVR and MBE based scheme has a RMSE of 2.78% in the estimation of decamer interaction energy against the parent QM method in a computationally efficient way.

References

May 26, 1995·Science·B Honig, A Nicholls
Jan 1, 1997·Annual Review of Physical Chemistry·C L Perrin, J B Nielson
Apr 12, 2001·Current Opinion in Structural Biology·T A Halgren, W Damm
Dec 26, 2001·Chemical Reviews·Grzegorz Chalasinski, Malgorzata M. Szcz&ecedil;śniak
Aug 16, 2002·Neural Computation·Chih-Chung Chang, Chih-Jen Lin
May 5, 2005·Proceedings of the National Academy of Sciences of the United States of America·William L Jorgensen, Julian Tirado-Rives
Oct 10, 2006·Physical Chemistry Chemical Physics : PCCP·J Grant HillHans-Joachim Werner
Nov 30, 2006·The Journal of Chemical Physics·Sergei Manzhos, Tucker Carrington
Mar 3, 2007·Science·Robert BukowskiAd van der Avoird
May 16, 2007·Physical Review Letters·Jörg Behler, Michele Parrinello
Oct 24, 2007·The Journal of Chemical Physics·Jeffery Ludwig, Dionisios G Vlachos
Nov 8, 2008·Physical Chemistry Chemical Physics : PCCP·Jeng-Da Chai, Martin Head-Gordon
Aug 28, 2009·The Journal of Chemical Physics·Roman M Balabin, Ekaterina I Lomakina
Oct 8, 2009·Physical Chemistry Chemical Physics : PCCP·Chris M HandleyPaul L A Popelier
Feb 6, 2010·The Journal of Physical Chemistry. a·Chris M Handley, Paul L A Popelier
Mar 20, 2010·Journal of Chemical Theory and Computation·Haibo YuBenoît Roux
May 20, 2011·Physical Chemistry Chemical Physics : PCCP·Roman M Balabin, Ekaterina I Lomakina
Sep 15, 2011·Physical Chemistry Chemical Physics : PCCP·Jörg Behler
Mar 10, 2012·Physical Review Letters·Matthias RuppO Anatole von Lilienfeld
Apr 6, 2013·The Journal of Physical Chemistry. a·Tobias Morawietz, Jörg Behler
Apr 25, 2014·Journal of Physics. Condensed Matter : an Institute of Physics Journal·J Behler
Jun 27, 2015·The Journal of Physical Chemistry Letters·Katja HansenAlexandre Tkatchenko
Jul 7, 2015·Journal of Chemical Theory and Computation·Pavlo O DralWalter Thiel
Sep 17, 2015·The Journal of Chemical Physics·Gregory R MeddersFrancesco Paesani
Nov 13, 2015·The Journal of Physical Chemistry. B·Daniel J Arismendi-ArrietaFrancesco Paesani
Nov 18, 2015·Journal of Chemical Theory and Computation·Raghunathan RamakrishnanO Anatole von Lilienfeld
Nov 18, 2015·Journal of Chemical Theory and Computation·Michael Gastegger, Philipp Marquetand
Nov 18, 2015·Journal of Chemical Theory and Computation·Tristan BereauO Anatole von Lilienfeld
Aug 12, 2014·Journal of Chemical Theory and Computation·Gregory R MeddersFrancesco Paesani
Sep 9, 2008·Journal of Chemical Theory and Computation·Michael G DarleyPaul L A Popelier
Jan 27, 2016·Journal of Chemical Theory and Computation·Kun Yao, John Parkhill
May 26, 2016·Journal of Chemical Theory and Computation·Timothy L Fletcher, Paul L A Popelier
Aug 19, 2016·Journal of Computational Chemistry·Stuart J DaviePaul L A Popelier
Oct 26, 2016·Journal of Chemical Theory and Computation·John F Ouyang, Ryan P A Bettens
Nov 9, 2016·The Journal of Chemical Physics·Jörg Behler
Jan 9, 2017·The Journal of Chemical Physics·Kun YaoJohn Parkhill

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Citations

Apr 22, 2019·The Journal of Chemical Physics·Emir KocerHakan Erturk
Feb 11, 2020·Frontiers in Chemistry·Tânia F G G Cova, Alberto A C C Pais

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Software Mentioned

SVR
NVT
Chem
PyBrain
Gromacs
MBE
kernlab
CVST

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