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Molecular dynamics simulations using non-rectangular, space-filling boxes like truncated octahedrons and rhombic dodecahedrons can improve parallel processing. This study explores their effect on diffusion and introduces a new correction formula validated with argon simulations.

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Area of Science:

  • Computational physics
  • Materials science
  • Chemical physics

Background:

  • Molecular dynamics simulations commonly use cubic or rectangular boxes.
  • Space-filling cells like truncated octahedrons and rhombic dodecahedrons offer advantages for biomolecular and liquid simulations.
  • Non-rectangular boxes are gaining popularity due to parallel processing benefits.

Purpose of the Study:

  • To investigate the impact of truncated octahedron and rhombic dodecahedron simulation boxes on diffusion.
  • To develop a theoretical hydrodynamic correction formula for diffusion in these non-rectangular boxes.
  • To validate the correction formula's range of validity through simulations.

Main Methods:

  • Theoretical derivation of a hydrodynamic correction formula for diffusion.
  • Performing molecular dynamics simulations using truncated octahedron and rhombic dodecahedron boxes.
  • Simulating argon at three different densities to evaluate the correction formula.

Main Results:

  • The study explores the effects of non-rectangular simulation boxes on diffusion for the first time.
  • A novel theoretical correction formula for diffusion in these boxes has been derived.
  • The formula's validity was assessed through molecular dynamics simulations of argon.

Conclusions:

  • Truncated octahedron and rhombic dodecahedron boxes are viable alternatives for molecular dynamics simulations.
  • The derived hydrodynamic correction formula accurately accounts for diffusion in these non-rectangular cells.
  • The findings support the increased use of non-rectangular boxes in molecular dynamics research.