Correction of diffusion calculations when using two types of non-rectangular simulation boxes in molecular simulations

  • Ting Cao
  • Xiangfei Ji
  • Jinpeng Wu
  • Shiju Zhang
  • Xiaofeng YangEmail author
Original Paper


Although simulation boxes used in molecular dynamics are normally chosen to be cubic or rectangular, two other cell shapes that are very familiar to crystallographers—the truncated octahedron and the rhombic dodecahedron—could also be used because they are also space-filling cells. Due to their spherical nature, these boxes have been intentionally applied in simulations of biomolecular solutions and liquid structures. Indeed, due to the advantages of running many molecular dynamic codes in parallel, simulations based on these non-rectangular boxes have been growing in popularity in recent years. In this work, the effects of using these two types of boxes on diffusion are explored for the first time, and an appropriate correction formula is derived theoretically within the framework of hydrodynamics. In addition, the range of validity for the correction formula is evaluated by performing molecular dynamic simulations on argon at three different densities.


Truncated octahedron Rhombic dodecahedron Diffusion coefficient Periodic boundary conditions 



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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of PhysicsNorth University of ChinaTaiyuanChina
  2. 2.School of Chemistry and Chemical EngineeringShanxi UniversityTaiyuanChina

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