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Small ionic radii limit time step in Martini 3 molecular dynamics simulations.

Balázs Fábián1, Sebastian Thallmair2, Gerhard Hummer1

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The Martini 3 force field

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Area of Science:

  • Computational chemistry
  • Molecular dynamics simulations
  • Biophysics

Background:

  • The Martini 3 force field offers improved protein solvation.
  • Accurate ion representation is crucial for molecular dynamics (MD) simulations.
  • Previous versions allowed larger time steps for lipid systems.

Purpose of the Study:

  • To investigate the time step limitations imposed by ion representation in Martini 3.
  • To develop a kinetic model for predicting MD simulation instabilities.
  • To identify strategies for increasing accessible time steps in Martini 3.

Main Methods:

  • Derivation of a quantitative kinetic model for time-integration instabilities.
  • Systematic variation of ion mass and bead size in simulations.
  • Analysis of static equilibrium and dynamic properties.

Main Results:

  • Tiny ion beads (TQ5) in Martini 3 limit time steps to 25 fs due to ion-water and ion-ion interactions.
  • Increasing ion mass or bead size enables time steps up to 40 fs with minimal impact on system properties.
  • Larger time steps improve configuration space exploration in Martini 3.

Conclusions:

  • Strategies exist to overcome Martini 3's time step limitations for ions.
  • The kinetic model aids in determining optimal time steps for efficient simulations.
  • Increased time steps enhance sampling efficiency in molecular dynamics.