Faster Simulations with a 5 fs Time Step for Lipids in the CHARMM Force Field

Journal of Chemical Theory and Computation
Karina OlesenHimanshu Khandelia

Abstract

The performance of all-atom molecular dynamics simulations is limited by an integration time step of 2 fs, which is needed to resolve the fastest degrees of freedom in the system, namely, the vibration of bonds and angles involving hydrogen atoms. The virtual interaction sites (VIS) method replaces hydrogen atoms by massless virtual interaction sites to eliminate these degrees of freedom while keeping intact nonbonded interactions and the explicit treatment of hydrogen atoms. We have modified the existing VIS algorithm for most lipids in the popular CHARMM36 force field by increasing the hydrogen atom masses at regular intervals in the lipid acyl chains and obtained lipid properties and pore formation free energies in very good agreement with those calculated in simulations without VIS. Our modified VIS scheme enables a 5 fs time step resulting in a significant performance gain for all-atom simulations of membranes. The method has the potential to make longer time and length scales accessible in all-atom simulations of membrane-protein complexes.

References

Mar 1, 1985·Physical Review A: General Physics·W G Hoover
Jan 25, 2003·Annual Review of Biophysics and Biomolecular Structure·Michael Edidin
Mar 21, 2008·Journal of Computational Chemistry·Sunhwan JoWonpil Im
Nov 18, 2009·Biophysical Journal·Qaiser Waheed, Olle Edholm
May 26, 2010·The Journal of Physical Chemistry. B·Jeffery B KlaudaRichard W Pastor
Feb 23, 2012·The Journal of Physical Chemistry. B·Joakim P M Jämbeck, Alexander P Lyubartsev
Feb 22, 2013·Proceedings of the National Academy of Sciences of the United States of America·Chen SongKornelius Zeth
Nov 2, 2013·Journal of Chemical Information and Modeling·Gunther LukatBjörn Sommer
Jan 15, 2014·Biophysical Journal·W F Drew BennettD Peter Tieleman
Apr 22, 2014·The Journal of Physical Chemistry. B·Arkadiusz MaciejewskiTomasz Rog
May 8, 2014·Journal of Chemical Theory and Computation·Callum J DicksonRoss C Walker
Aug 1, 2014·PLoS Computational Biology·Song KeAnna Stary-Weinzinger
Aug 19, 2014·Journal of Computational Chemistry·Emilia L WuWonpil Im
Mar 21, 2015·Journal of Chemical Information and Modeling·Tobias LinderAnna Stary-Weinzinger
Nov 20, 2015·Journal of Chemical Theory and Computation·Bastien LoubetHimanshu Khandelia
Aug 14, 2012·Journal of Chemical Theory and Computation·Joakim P M Jämbeck, Alexander P Lyubartsev
Oct 12, 2010·Journal of Chemical Theory and Computation·Lorant Janosi, Alemayehu A Gorfe
Mar 26, 2016·Journal of Chemical Theory and Computation·Josef MelcrPavel Jungwirth
Apr 6, 2017·Journal of Chemical Theory and Computation·Jochen S Hub, Neha Awasthi
Jan 9, 2018·The Journal of Physical Chemistry. B·Jigneshkumar Dahyabhai PrajapatiUlrich Kleinekathöfer

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Citations

Sep 4, 2019·Nature Communications·Simon R BushellElisabeth P Carpenter
Sep 16, 2020·Nature Microbiology·Justin C DemeSusan M Lea
Jan 8, 2020·Nature Structural & Molecular Biology·Valerie E PyePeter Cherepanov
Feb 2, 2020·Nature Communications·Igor TascónInga Hänelt
Jul 28, 2018·Biochimica Et Biophysica Acta. Biomembranes·Alexandra Schumann-Gillett, Megan L O'Mara
Aug 17, 2021·The Journal of Physical Chemistry. B·Sebastian ThallmairSiewert J Marrink
Feb 21, 2019·Chemical Reviews·Alison N LeonardJeffery B Klauda
Jul 3, 2019·Journal of Chemical Theory and Computation·Curtis BalusekJames C Gumbart
May 27, 2020·Langmuir : the ACS Journal of Surfaces and Colloids·Flaviyan Jerome Irudayanathan, Shikha Nangia
Nov 24, 2018·Journal of Chemical Theory and Computation·Jaewoon JungYuji Sugita
Sep 7, 2021·The Journal of Physical Chemistry. B·Archita Maiti, Snehasis Daschakraborty

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