Momentum removal to obtain the position-dependent diffusion constant in constrained molecular dynamics simulation

Area of Science:

• Computational physics and chemistry
• Materials science
• Biophysics

Background:

• Mass transport in heterogeneous systems like membranes is crucial.
• Molecular dynamics (MD) simulations are key tools for studying diffusion.
• The Marrink-Berendsen (MB) method is widely used for calculating position-dependent diffusion coefficients.

Purpose of the Study:

• To theoretically investigate the effect of center-of-mass velocity removal on diffusion coefficient calculations.
• To provide practical guidelines for selecting optimal parameters in MD simulations.
• To validate theoretical predictions with computational experiments.

Main Methods:

• Theoretical analysis of the Marrink-Berendsen (MB) method.
• Molecular dynamics (MD) simulations incorporating the Ewald method for Coulombic interactions.
• Analysis of the autocorrelation function of forces on fixed molecules.

Main Results:

• The period of center-of-mass velocity removal significantly affects diffusion coefficient values.
• Theoretical predictions accurately describe the impact of this operation.
• MD calculations confirm the theoretical findings.

Conclusions:

• Understanding the influence of velocity removal is essential for accurate diffusion coefficient estimation.
• The study offers practical guidance for selecting appropriate $$ values in MB and Woolf-Roux methods.
• This work enhances the reliability of MD simulations for mass transport studies in complex systems.