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On Reaction Coordinate Optimality.

Sergei V Krivov1

  • 1School of Molecular and Cellular Biology, Leeds University, Leeds, United Kingdom.

Journal of Chemical Theory and Computation
|November 22, 2015
PubMed
Summary

An optimal reaction coordinate accurately describes molecular dynamics when its free energy profile is constant. This finding enables exact equilibrium flux calculations and distinguishes linear from sub-linear mean square displacement growth.

Area of Science:

  • Computational chemistry
  • Statistical mechanics
  • Molecular dynamics

Background:

  • Defining accurate reaction coordinates is crucial for understanding molecular dynamics.
  • Suboptimal coordinates can lead to inaccurate descriptions of system behavior.

Purpose of the Study:

  • To establish criteria for an optimal reaction coordinate.
  • To demonstrate the implications of an optimal coordinate for calculating dynamic properties.

Main Methods:

  • Analysis of free energy profiles using length-weighted transitions.
  • Comparison of trajectory projections onto optimal and suboptimal coordinates.
  • Application to model systems including proteins and peptides.

Main Results:

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  • An optimal reaction coordinate yields a constant, position- and sampling-independent free energy profile.
  • Equilibrium flux can be precisely calculated via diffusion on the optimal coordinate's free energy profile.
  • Mean square displacement grows linearly with time for trajectories on optimal coordinates, versus sub-linearly for suboptimal ones.

Conclusions:

  • The developed criterion provides a rigorous method for validating reaction coordinates.
  • Optimal reaction coordinates simplify the analysis of molecular dynamics and kinetics.
  • The findings are broadly applicable across various complex molecular systems.