Modeling diffusive dynamics in adaptive resolution simulation of liquid water

The Journal of Chemical Physics
Silvina MatysiakLuigi Delle Site

Abstract

We present a dual-resolution molecular dynamics (MD) simulation of liquid water employing a recently introduced Adaptive Resolution Scheme (AdResS). The spatially adaptive molecular resolution procedure allows for changing from a coarse-grained to an all-atom representation and vice versa on-the-fly. In order to find the most appropriate coarse-grained water model to be employed with AdResS, we first study the accuracy of different coarse-grained water models in reproducing the structural properties of the all-atom system. Typically, coarse-grained molecular models have a higher diffusion constant than the corresponding all-atom models due to the reduction in degrees of freedom (DOFs) upon coarse-graining that eliminates the fluctuating forces associated with those integrated-out molecular DOFs. Here, we introduce the methodology to obtain the same diffusional dynamics across different resolutions. We show that this approach leads to the correct description of the here relevant structural, thermodynamical, and dynamical properties, i.e., radial distribution functions, pressure, temperature, and diffusion, of liquid water at ambient conditions.

References

Oct 1, 1995·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·A P Lyubartsev, A Laaksonen
Feb 24, 2001·Nature·J R Errington, P G Debenedetti
Jan 24, 2002·Proceedings of the National Academy of Sciences of the United States of America·Margaret S CheungJosé N Onuchic
Nov 13, 2002·Proceedings of the National Academy of Sciences of the United States of America·Samir Kumar PalAhmed H Zewail
Aug 20, 2003·Journal of Computational Chemistry·Dirk ReithFlorian Müller-Plathe
Dec 20, 2003·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Thomas SoddemannKurt Kremer
Apr 20, 2005·The Journal of Chemical Physics·Jeremy M Moix, Rigoberto Hernandez
May 5, 2005·Annual Review of Biophysics and Biomolecular Structure·Ken A DillBarbara Hribar-Lee
May 25, 2005·The Journal of Chemical Physics·Matej Praprotnik, Dusanka Janezic
Oct 15, 2005·The Journal of Chemical Physics·Sergei Izvekov, Gregory A Voth
Dec 27, 2005·The Journal of Chemical Physics·Matej PraprotnikKurt Kremer
Dec 31, 2005·Physical Review Letters·Marilisa NeriPaolo Carloni
Jan 6, 2006·The Journal of Chemical Physics·J A BackerP D Iedema
Jan 6, 2006·The Journal of Chemical Physics·Cameron F Abrams
Feb 21, 2006·Physical Review Letters·Edward LymanDaniel M Zuckerman
Apr 12, 2006·Physical Review Letters·Silvina MatysiakCecilia Clementi
Aug 16, 2006·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Matej PraprotnikKurt Kremer
Sep 9, 2006·Journal of Molecular Biology·Silvina Matysiak, Cecilia Clementi
Oct 10, 2006·Physical Review Letters·G De FabritiisP V Coveney
Oct 25, 2006·The Journal of Chemical Physics·Sergei Izvekov, Gregory A Voth
Mar 16, 2007·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Matej PraprotnikLuigi Delle Site
Apr 14, 2007·The Journal of Chemical Physics·Matej PraprotnikKurt Kremer
Apr 21, 2007·The Journal of Chemical Physics·Margaret E JohnsonArd A Louis
Nov 13, 2007·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Luigi Delle Site
May 1, 2007·Journal of Chemical Theory and Computation·Bernd EnsingMichele Parrinello

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Citations

Aug 14, 2009·The Journal of Chemical Physics·Teemu MurtolaIlpo Vattulainen
Mar 8, 2013·The Journal of Chemical Physics·Xin Yong, Lucy T Zhang
Dec 22, 2010·The Journal of Chemical Physics·Bradley P LambethLuigi Delle Site
Aug 3, 2012·The Journal of Chemical Physics·Sereina Riniker, Wilfred F van Gunsteren
Mar 26, 2008·The Journal of Chemical Physics·Rafael Delgado-BuscalioniMatej Praprotnik
Jan 12, 2010·The Journal of Chemical Physics·Rafael Delgado-BuscalioniMatej Praprotnik
May 13, 2010·The Journal of Chemical Physics·Antonios SamiotakisMargaret S Cheung
Dec 28, 2007·Current Opinion in Structural Biology·Cecilia Clementi
May 24, 2015·The Journal of Chemical Physics·Aoife C FogartyKurt Kremer
Apr 26, 2016·The Journal of Physical Chemistry. B·Francesca Stanzione, Arthi Jayaraman
Feb 2, 2015·The Journal of Chemical Physics·Nikolai D PetsevM Scott Shell
Jul 8, 2016·Journal of Chemical Theory and Computation·Karsten KreisAoife C Fogarty
Aug 1, 2016·The Journal of Chemical Physics·Karsten Kreis, Raffaello Potestio
Jan 28, 2017·Physical Chemistry Chemical Physics : PCCP·Christian Krekeler, Luigi Delle Site
Sep 15, 2017·European Biophysics Journal : EBJ·Julija ZavadlavMatej Praprotnik
Mar 29, 2014·Journal of Computational Chemistry·Nicodemo Di PasqualePaola Carbone
Aug 25, 2010·Physical Chemistry Chemical Physics : PCCP·Steven O NielsenBernd Ensing
Jul 3, 2017·The Journal of Chemical Physics·Raffaele FiorentiniAoife C Fogarty
Jul 17, 2018·The Journal of Chemical Physics·Christian KrekelerLuigi Delle Site
Jan 27, 2011·Physical Chemistry Chemical Physics : PCCP·Marcus BöckmannNikos L Doltsinis
Sep 25, 2017·The Journal of Chemical Physics·Julija Zavadlav, Matej Praprotnik
Nov 4, 2020·The Journal of Chemical Physics·S ThalerJ Zavadlav
Aug 1, 2008·Journal of Chemical Theory and Computation·Michele CascellaMatteo Dal Peraro
Dec 8, 2009·Journal of Chemical Theory and Computation·Sergei Izvekov, Gregory A Voth
May 29, 2018·Journal of Chemical Theory and Computation·Justin ChenCecilia Clementi
Oct 9, 2012·Journal of Chemical Theory and Computation·Leonardo DarréSergio Pantano
Nov 8, 2011·Journal of Chemical Theory and Computation·Zhe WuArun Yethiraj
Apr 10, 2014·The Journal of Physical Chemistry. B·Jianguo Zhang, Hongxia Guo
Nov 12, 2013·Journal of Chemical Theory and Computation·Anu NagarajanSilvina Matysiak

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Software Mentioned

AdResS
TIP3P

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