{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/an-orthoboxy-method-for-various-alternative","title":"An OrthoBoXY-Method for Various Alternative Box Geometries","arxiv_id":"2310.01026","date":"2023-10-02","proceeding":null,"authors":["Johanna Busch","Dietmar Paschek"],"abstract":"We have shown in a recent contribution [J. Phys. Chem.B 127, 7983-7987 (2023)] that for molecular dynamics (MD) simulations of isotropic fluids based on orthorhombic periodic boundary conditions with \"magic\" box length ratios of $L_z/L_x\\!=\\!L_z/L_y\\!=\\!2.7933596497$, the computed self-diffusion coefficients $D_x$ and $D_y$ in $x$- and $y$-direction become system size independent. They thus represent the true self-diffusion coefficient $D_0\\!=\\!(D_x+D_y)/2$, while the shear viscosity can be determined from diffusion coefficients in $x$-, $y$-, and $z$-direction, using the expression $\\eta\\!=\\!k_\\mathrm{B}T\\cdot 8.1711245653/[3\\pi L_z(D_{x}+D_{y}-2D_z)]$. Here we present a more generalized version of this \"OrthoBoXY\"-approach, which can be applied to any orthorhombic MD box. We would like to test, whether it is possible to improve the efficiency of the approach by using a shape more akin to the cubic form, albeit with different box-length ratios $L_x/L_z\\!\\neq\\! L_y/L_z$ and $L_x\\!<\\!L_y\\!<\\!L_z$. We use simulations of systems of 1536 TIP4P/2005 water molecules as a benchmark and explore different box-geometries to determine the influence of the box shape on the computed statistical uncertainties for $D_0$ and $\\eta$. Moreover, another \"magical\" set of box-length ratios is discovered with $L_y/L_z\\!=\\!0.57804765578$ and $L_x/L_z\\!=\\!0.33413909235$, where the self-diffusion coefficient in $x$-direction becomes system size independent, such that $D_0\\!=\\!D_x$.","url_abs":"https://arxiv.org/abs/2310.01026v2","url_pdf":"https://arxiv.org/pdf/2310.01026v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"links_only","authors_date_abstract":"arXiv metadata, CC0 1.0 (https://info.arxiv.org/help/license), from the Kaggle arXiv metadata snapshot of 2026-09-12"},"code_links":[{"paper_slug":"an-orthoboxy-method-for-various-alternative","repo_url":"https://github.com/paschek-lab/orthoboxy","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}