Calculating Iso-Committor Surfaces as Optimal Reaction Coordinates with Milestoning

Area of Science:

• Computational chemistry
• Molecular dynamics
• Chemical kinetics

Background:

• Reaction coordinates are crucial for understanding molecular processes, offering insights into reaction progress.
• Iso-committor surfaces represent the optimal reaction coordinate for accurate analysis.
• Current methods may be computationally intensive or lack efficiency.

Purpose of the Study:

• To develop and present an efficient algorithm for computing a sequence of iso-committor surfaces.
• To establish a robust method for identifying optimal reaction coordinates.
• To facilitate the calculation of free energies and reaction rates.

Main Methods:

• The algorithm analyzes Milestoning (MS) results to determine the committor function.
• It leverages transition probabilities between milestones, bypassing the need for transition times.
• Efficient computation of sequential iso-committor surfaces is achieved.

Main Results:

• The developed algorithm efficiently computes optimal reaction coordinates based on iso-committor surfaces.
• The method demonstrates applicability across diverse systems, including potentials, peptides, and aggregation processes.
• Accurate committor functions are derived solely from transition probabilities.

Conclusions:

• The presented algorithm offers an efficient and accurate approach to determine optimal reaction coordinates.
• This method enhances the analysis of molecular processes and aids in free energy calculations.
• The iso-committor surface computation is a valuable tool for computational chemistry research.