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Rare Event Kinetics from Adaptive Bias Enhanced Sampling.

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We present on-the-fly probability enhanced sampling (OPES) flooding, a new method for molecular dynamics simulations. This technique accurately calculates rare event kinetics by ensuring simulation bias does not exceed the effective barrier height.

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Area of Science:

  • Computational Chemistry
  • Biophysics
  • Statistical Mechanics

Background:

  • Calculating rare event kinetics in molecular dynamics is computationally challenging.
  • Enhanced sampling methods are crucial for overcoming energy barriers in simulations.
  • On-the-the-fly probability enhanced sampling (OPES) has been developed for free energy calculations.

Purpose of the Study:

  • Introduce and detail the novel on-the-fly probability enhanced sampling (OPES) flooding method.
  • Apply OPES flooding to calculate kinetics of rare events in molecular systems.
  • Investigate the impact of bias and collective variables on kinetic calculations.

Main Methods:

  • Developed and implemented the OPES flooding enhanced sampling technique.
  • Applied OPES flooding to a 2D double-well potential, alanine dipeptide, and chignolin polypeptide.
  • Performed extensive tests to validate the accuracy and efficiency of the method.

Main Results:

  • Demonstrated that OPES flooding accurately calculates rare event kinetics from atomistic molecular dynamics.
  • Showed that bias must not exceed the effective barrier height for accurate rate calculations.
  • Explored the computation of rates using suboptimal order parameters.

Conclusions:

  • OPES flooding is a powerful tool for determining rare event kinetics in complex molecular systems.
  • Optimizing parameter combinations is key to achieving accurate results with limited computational resources.
  • The study provides guidelines for applying OPES flooding effectively in molecular simulations.