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  Classical Molecular Dynamics with Mobile Protons

Lazaridis, T., & Hummer, G. (2017). Classical Molecular Dynamics with Mobile Protons. Journal of Chemical Information and Modeling, 57(11), 2833-2845. doi:10.1021/acs.jcim.7b00603.

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 Creators:
Lazaridis, Themis1, 2, Author
Hummer, Gerhard3, Author                 
Affiliations:
1Department of Chemistry, City College of New York/CUNY, 160 Convent Avenue, New York, New York 10031, United States, ou_persistent22              
2Graduate Programs in Chemistry, Biochemistry & Physics, Graduate Center, City University of New York, 365 Fifth Ave, New York, New York 10016, United States, ou_persistent22              
3Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society, ou_2068292              

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 Abstract: An important limitation of standard classical molecular dynamics simulations is the inability to make or break chemical bonds. This restricts severely our ability to study processes that involve even the simplest of chemical reactions, the transfer of a proton. Existing approaches for allowing proton transfer in the context of classical mechanics are rather cumbersome and have not achieved widespread use and routine status. Here we reconsider the combination of molecular dynamics with periodic stochastic proton hops. To ensure computational efficiency, we propose a non-Boltzmann acceptance criterion that is heuristically adjusted to maintain the correct or desirable thermodynamic equilibria between different protonation states and proton transfer rates. Parameters are proposed for hydronium, Asp, Glu, and His. The algorithm is implemented in the program CHARMM and tested on proton diffusion in bulk water and carbon nanotubes and on proton conductance in the gramicidin A channel. Using hopping parameters determined from proton diffusion in bulk water, the model reproduces the enhanced proton diffusivity in carbon nanotubes and gives a reasonable estimate of the proton conductance in gramicidin A.

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Language(s): eng - English
 Dates: 2017-10-102017-11-022017-11-27
 Publication Status: Issued
 Pages: 13
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1021/acs.jcim.7b00603
 Degree: -

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Title: Journal of Chemical Information and Modeling
Source Genre: Journal
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Publ. Info: Washington, D.C. : American Chemical Society
Pages: - Volume / Issue: 57 (11) Sequence Number: - Start / End Page: 2833 - 2845 Identifier: ISSN: 1549-9596
CoNE: https://pure.mpg.de/cone/journals/resource/954925465222