SKM 2023 – wissenschaftliches Programm
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BP: Fachverband Biologische Physik
BP 27: Computational Biophysics II
BP 27.9: Vortrag
Donnerstag, 30. März 2023, 17:15–17:30, BAR 0106
Unwrapping trajectories of constant-pressure molecular dynamics simulations — •Jakob Tómas Bullerjahn1, Sören von Bülow2, Jérôme Hénin3, and Gerhard Hummer1,4 — 1Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany — 2Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark — 3Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, CNRS, Paris, France — 4Institute of Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany
In molecular dynamics simulations at constant pressure, the size and shape of the periodic simulation box fluctuate with time. Special care is thus required when a particle trajectory is unwrapped from a projection into the central box under periodic boundary conditions into a trajectory in full three-dimensional space, e.g., for the calculation of diffusion coefficients. Here, we review and compare different schemes proposed for trajectory unwrapping, and specify the respective rewrapping scheme to put an unwrapped trajectory back into the central box. On this basis, we then identify a scheme in which the wrapped and unwrapped trajectory are mutually consistent and in which the statistical properties of the trajectory are preserved. We conclude with advice on best practice for the consistent unwrapping of constant-pressure simulation trajectories.