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Characterization of Biological Membranes

Structure and Dynamics

Ed. by Nieh, Mu-Ping / Heberle, Frederick A. / Katsaras, John

With contrib. by Bowerman, Charles / Bozelli Junior, José Carlos / Brown, Michael F. / Butler, Paul D. / Chan, Chun / Cheng, Xiaolin / Cherniavskyi, Yevhen / Cheung, Eugene / Chini, Corryn E. / Craig, Andrew F. / Dabney-Smith, Carole / Davis, James H. / Dimova, Rumiana / DiPasquale, Mitchell / Eells, Rebecca / Epand, Richard M. / Fisher, Alessandro / Frank, Kilian / Gorman, Brittney L. / Harroun, Thad A. / Heinrich, Frank / Hoogerheide, David P. / Kelly, Elizabeth G. / Kienzle, Paul A. / Kiessling, Volker / Komorowski, Karlo / Konkolewicz, Dominik / Kraft, Mary / Kučerka, Norbert / Li, Ying / London, Erwin / Lorigan, Gary A. / Lösche, Mathias / Majkrzak, Charles F. / Marquardt, Drew / Nagao, Michihiro / Nguyen, Michael H.L. / Nickels, Jonathan / Poloni, Laura / Sahu, Indra D. / Salditt, Tim / Schick, Michael / Schmidt, Miranda / Shen, Zhingiang / Steinkühler, Jan / Tamm, Lukas K. / Tieleman, Peter / Uhríková, Daniela / Won, Amy / Xia, Yan / Ye, Huilin / Yeager, Ashley N. / Yip, Christopher M.

Series:De Gruyter STEM

eBook (PDF)
Publication Date:
July 2019
Copyright year:
2019
ISBN
978-3-11-054465-7
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19. Simulations of biological membranes with the Martini model

Cherniavskyi, Yevhen / Tieleman, D. Peter

Abstract

Molecular dynamics (MD) simulations are an extremely useful class of methods for characterization of biological membranes. Constant increase of computer power and simulation software efficiency during the past few decades significantly pushed the boundaries in the field. With modern all-atom force fields, one can easily simulate smallmembrane systemusing desktop computer and obtain atomistic level of structural detail. But despite this progress, all-atom force fields introduce pose practical limits on the systemsizes and timescales accessible for MD. Less detailed, coarsegrained force fields significantly reduce the amount of computer power required for simulations, but this speedup comes at a cost of structural detail. The Martini model is the most widely used coarse-grain force field for MD simulations of biological membranes and membrane proteins. While retaining significant chemical detail of the lipids,Martini reduces the computational cost of simulations up to 103 times compared to all-atom force fields. This enables simulations of complex behavior of mixed membranes by MD. Here, we begin with an overview of the Martini model, its advantages and limitations in the context of MD simulations of biologicalmembranes, followed by recent examples of large-scale simulations of mixed membrane systems.

Citation Information

Yevhen Cherniavskyi, D. Peter Tieleman (2019). 19. Simulations of biological membranes with the Martini model. In Mu-Ping Nieh, Frederick A. Heberle, John Katsaras (Eds.), Characterization of Biological Membranes: Structure and Dynamics (pp. 551–568). Berlin, Boston: De Gruyter. https://doi.org/10.1515/9783110544657-019

Book DOI: https://doi.org/10.1515/9783110544657

Online ISBN: 9783110544657

© 2019 Walter de Gruyter GmbH, Berlin/Munich/BostonGet Permission

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