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

The Journal of Chemical Physics
Sören von BülowGerhard Hummer

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.

References

Oct 30, 2014·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Christian L VestergaardHenrik Flyvbjerg
Jul 17, 2020·The Journal of Chemical Physics·Jakob Tómas BullerjahnGerhard Hummer

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Citations

Jul 17, 2020·The Journal of Chemical Physics·Jakob Tómas BullerjahnGerhard Hummer
Dec 1, 2020·ACS Omega·Jan M Antosiewicz, Maciej Długosz
Aug 28, 2021·Journal of Chemical Theory and Computation·Paul Smith, Christian D Lorenz
Sep 16, 2021·The Journal of Physical Chemistry. B·Aysenur IscenKurt Kremer

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