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Finite-size effects in molecular dynamics simulations of protein and nucleic acid rotational dynamics can be corrected. A hydrodynamic correction removes box-size dependence, yielding accurate hydrodynamic radii matching experimental data.

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Area of Science:

  • Biophysics
  • Computational Chemistry
  • Molecular Dynamics

Background:

  • Molecular dynamics (MD) simulations are crucial for understanding biomolecular behavior.
  • Simulations under periodic boundary conditions can introduce artifacts, such as finite-size effects.
  • Accurate determination of rotational dynamics is essential for protein and nucleic acid function.

Purpose of the Study:

  • To identify and correct finite-size effects in MD simulations of rotational dynamics.
  • To develop a method for accurate calculation of rotational diffusion coefficients.
  • To validate the correction method with experimental data.

Main Methods:

  • Utilized molecular dynamics simulations with periodic boundary conditions.
  • Applied a hydrodynamic correction (kBT/6ηV) to rotational diffusion coefficients.
  • Calculated hydrodynamic radii for myoglobin and B-DNA dodecamer.

Main Results:

  • Demonstrated significant finite-size effects in simulated rotational dynamics.
  • The hydrodynamic correction successfully removed box-size dependence.
  • Obtained hydrodynamic radii in excellent agreement with experimental values.

Conclusions:

  • The proposed hydrodynamic correction is effective in mitigating finite-size effects in MD simulations.
  • This method enables more accurate predictions of biomolecular rotational dynamics.
  • The findings enhance the reliability of MD simulations for biophysical studies.