rs@md: Introducing Reactive Steps at the Molecular Dynamics Simulation Level.

Area of Science:

• Computational Chemistry
• Molecular Dynamics Simulations
• Chemical Kinetics

Background:

• Molecular dynamics (MD) simulations are crucial for studying molecular behavior.
• Simulating chemical reactions within MD requires handling transitions between reactant and product states.
• Existing methods may not accurately capture both thermodynamics and kinetics of reactive processes.

Purpose of the Study:

• To develop a novel method for extending molecular dynamics simulations with reactive steps.
• To enable physically correct transition probabilities and instant force field exchange during simulations.
• To ensure accurate thermodynamic and kinetic properties of reactive systems.

Main Methods:

• Introduced 'reactive steps' into molecular dynamics simulations.
• Derived mathematical framework for computing acceptance probability from molecular reaction rates.
• Developed a modular simulation program for reactive step molecular dynamics.
• Applied the method to a model system of associating/dissociating Lennard-Jones particles.

Main Results:

• The developed method allows for physically correct transition probabilities during reactive steps.
• The approach enables instant exchange of force fields during simulations.
• Demonstrated accurate recovery of thermodynamics and proper kinetics (time evolution) in a model system.
• Comparison with Nagaoka et al.'s Monte Carlo approach validated the method's effectiveness.

Conclusions:

• The proposed reactive step molecular dynamics approach accurately simulates chemical transformations.
• The method ensures correct thermodynamic and kinetic behavior, crucial for understanding chemical reactions.
• The modular design allows integration with existing molecular dynamics programs.