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Unwrapping NPT Simulations to Calculate Diffusion Coefficients.

Jakob Tómas Bullerjahn1, Sören von Bülow2, Maziar Heidari1

  • 1Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.

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Summary

Molecular dynamics simulations require careful trajectory unwrapping in the NPT ensemble. This study presents a consistent method for unwrapping and rewrapping trajectories, ensuring accurate diffusion coefficient calculations.

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Area of Science:

  • Computational chemistry
  • Statistical mechanics
  • Molecular modeling

Background:

  • Molecular dynamics (MD) simulations in the NPT ensemble involve fluctuating box sizes due to barostat adjustments.
  • This box rescaling can cause unbounded position displacements for particle images far from the origin.
  • Accurate unwrapping of particle trajectories is crucial for calculating properties like translational diffusion coefficients.

Purpose of the Study:

  • To review and compare existing schemes for unwrapping particle trajectories from periodic boundary conditions.
  • To introduce corresponding rewrapping schemes for returning trajectories to the central box.
  • To identify a robust scheme for calculating diffusion coefficients from NPT simulations.

Main Methods:

  • Comparative analysis of different trajectory unwrapping algorithms.
  • Development and specification of complementary rewrapping schemes.
  • Validation of a chosen unwrapping/rewrapping scheme for diffusion coefficient calculation.

Main Results:

  • Different unwrapping schemes exhibit varying degrees of accuracy and consistency.
  • A specific unwrapping and rewrapping scheme is identified as mutually consistent.
  • The proposed scheme preserves the statistical properties of the trajectory data.

Conclusions:

  • Consistent unwrapping and rewrapping are essential for accurate analysis of NPT simulations.
  • The recommended best practice ensures reliable calculation of translational diffusion coefficients.
  • This work provides guidance for researchers using constant-pressure molecular dynamics simulations.