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Density artefacts at interfaces caused by multiple time-step effects in molecular dynamics simulations.

Dominik Sidler1, Marc Lehner1, Simon Frasch1

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Multiple time-step molecular dynamics (MD) simulations can cause artificial density increases at interfaces. Using single-range nonbonded interactions or stochastic dynamics thermostats resolves these artifacts, unlike twin-range schemes with certain thermostats.

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Area of Science:

  • Computational chemistry
  • Biophysics
  • Molecular modeling

Background:

  • Molecular dynamics (MD) simulations are crucial for understanding biomolecular processes.
  • Multiple time-step methods accelerate MD simulations but can introduce numerical artifacts.
  • Interfaces between polar and apolar media, like biological membranes, are common in simulations.

Purpose of the Study:

  • To investigate the impact of multiple time-step algorithms on MD simulations at polar-apolar interfaces.
  • To identify specific algorithms and thermostat combinations that cause numerical artifacts.

Main Methods:

  • MD simulations were performed to analyze multiple time-step integration schemes.
  • The twin-range (TR) scheme and impulse-wise reversible reference system propagation algorithm (RESPA) were evaluated.
  • Comparisons were made with single-range (SR) treatment and stochastic dynamics thermostats.

Main Results:

  • The TR scheme with weak coupling or Nosé-Hoover (chain) thermostats induced artificial density increases at interfaces.
  • RESPA integration shifted density artifacts to larger outer time steps.
  • SR treatment and stochastic dynamics thermostats eliminated density issues for extended periods.

Conclusions:

  • Twin-range (TR) schemes are not recommended with weak coupling or Nosé-Hoover (chain) thermostats for simulations at interfaces.
  • Careful selection of integration methods and thermostats is essential to avoid numerical artifacts in MD simulations.
  • Single-range (SR) methods offer a robust alternative for accurate simulations at complex interfaces.