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

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von Bülow,  Sören
Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society;

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Bullerjahn,  Jakob T.
Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society;

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Hummer,  Gerhard
Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society;
Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany;

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Citation

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.


Cite as: http://hdl.handle.net/21.11116/0000-0006-BA45-B
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.