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  Systematic errors in diffusion coefficients from long-time molecular dynamics simulations at constant pressure

von Bülow, S., Bullerjahn, J. T., & Hummer, G. (2020). Systematic errors in diffusion coefficients from long-time molecular dynamics simulations at constant pressure. The Journal of Chemical Physics, 153(2): 021101. doi:10.1063/5.0008316.

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von Bülow, Sören1, Author              
Bullerjahn, Jakob T.1, Author              
Hummer, Gerhard1, 2, Author              
Affiliations:
1Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society, ou_2068292              
2Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany, ou_persistent22              

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 Abstract: In molecular dynamics simulations under periodic boundary conditions, particle positions are typically wrapped into a reference box. For diffusion coefficient calculations using the Einstein relation, the particle positions need to be unwrapped. Here, we show that a widely used heuristic unwrapping scheme is not suitable for long simulations at constant pressure. Improper accounting for box-volume fluctuations creates, at long times, unphysical trajectories and, in turn, grossly exaggerated diffusion coefficients. We propose an alternative unwrapping scheme that resolves this issue. At each time step, we add the minimal displacement vector according to periodic boundary conditions for the instantaneous box geometry. Here and in another paper [J. T. Bullerjahn, S. von Bülow, and G. Hummer, J. Chem. Phys. 153, 024116 (2020)], we apply the new unwrapping scheme to extensive molecular dynamics and Brownian dynamics simulation data. We provide practitioners with a formula to assess if and by how much earlier results might have been affected by the widely used heuristic unwrapping scheme.

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Language(s): eng - English
 Dates: 2020-03-202020-05-212020-07-092020-07-14
 Publication Status: Published in print
 Pages: 6
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1063/5.0008316
 Degree: -

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Title: The Journal of Chemical Physics
  Other : J. Chem. Phys.
Source Genre: Journal
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Publ. Info: Woodbury, N.Y. : American Institute of Physics
Pages: - Volume / Issue: 153 (2) Sequence Number: 021101 Start / End Page: - Identifier: ISSN: 0021-9606
CoNE: https://pure.mpg.de/cone/journals/resource/954922836226