Reaction coordinates are vital tools for qualitative and quantitative analysis of molecular processes. They provide a simple picture of reaction progress and essential input for calculations of free energies and rates. Iso-committor surfaces are considered the optimal reaction coordinate. We present an algorithm to compute efficiently a sequence of isocommittor surfaces. These surfaces are considered an optimal reaction coordinate. The algorithm analyzes Milestoning results to determine the committor function. It requires only the transition probabilities between the milestones, and not transition times. We discuss the following numerical examples: (i) a transition in the Mueller potential; (ii) a conformational change of a solvated peptide...
We propose a new method for calculating all stationary states, including saddle points of all orders...
A basic problem when calculating reaction rates using the reactive flux method is the introduction o...
The reaction path of a mechanically induced chemical transformation changes under stress. It is well...
The mechanism of transition (reaction coordinate) during an activated process is best described in t...
The dynamic behavior of complex systems with many degrees of freedom is often analyzed by projection...
The molecular mechanism of a reaction in solution is reflected in its transition-state ensemble and ...
A new method for optimizing transition state and minima structures using redundant internal coordina...
An algorithm is presented for determining multi dimensional reaction coordinates between two known c...
State of the art realistic simulations of complex atomic processes commonly produce trajectories of ...
The characteristics of a chemical reaction are largely determined by the molecular structures associ...
In molecular simulations, the identification of suitable reaction coordinates is central to both the...
The characteristics of a chemical reaction are largely determined by the molecular structures associ...
Given two metastable states A and B of a biomolecular system, the problem is to calculate the likely...
The identification of meaningful reaction coordinates plays a key role in the study of complex molec...
iii Geometry optimization is a key step in the computational modeling of chemical reactions because ...
We propose a new method for calculating all stationary states, including saddle points of all orders...
A basic problem when calculating reaction rates using the reactive flux method is the introduction o...
The reaction path of a mechanically induced chemical transformation changes under stress. It is well...
The mechanism of transition (reaction coordinate) during an activated process is best described in t...
The dynamic behavior of complex systems with many degrees of freedom is often analyzed by projection...
The molecular mechanism of a reaction in solution is reflected in its transition-state ensemble and ...
A new method for optimizing transition state and minima structures using redundant internal coordina...
An algorithm is presented for determining multi dimensional reaction coordinates between two known c...
State of the art realistic simulations of complex atomic processes commonly produce trajectories of ...
The characteristics of a chemical reaction are largely determined by the molecular structures associ...
In molecular simulations, the identification of suitable reaction coordinates is central to both the...
The characteristics of a chemical reaction are largely determined by the molecular structures associ...
Given two metastable states A and B of a biomolecular system, the problem is to calculate the likely...
The identification of meaningful reaction coordinates plays a key role in the study of complex molec...
iii Geometry optimization is a key step in the computational modeling of chemical reactions because ...
We propose a new method for calculating all stationary states, including saddle points of all orders...
A basic problem when calculating reaction rates using the reactive flux method is the introduction o...
The reaction path of a mechanically induced chemical transformation changes under stress. It is well...