Eur. Phys. J. B (2021) 94: 223
https://doi.org/10.1140/epjb/s10051-021-00233-5

Topical Review - Computational Methods

Reaction coordinates in complex systems-a perspective

¹ Department of Chemistry, New York University, 10003, New York, NY, USA
² Fachbereich Physik, Freie Universität Berlin, 14195, Berlin, Germany

^a jutta.rogal@nyu.edu

Received: 4 August 2021
Accepted: 26 October 2021
Published online: 12 November 2021

Abstract

In molecular simulations, the identification of suitable reaction coordinates is central to both the analysis and sampling of transitions between metastable states in complex systems. If sufficient simulation data are available, a number of methods have been developed to reduce the vast amount of high-dimensional data to a small number of essential degrees of freedom representing the reaction coordinate. Likewise, if the reaction coordinate is known, a variety of approaches have been proposed to enhance the sampling along the important degrees of freedom. Often, however, neither one nor the other is available. One of the key questions is therefore, how to construct reaction coordinates and evaluate their validity. Another challenges arises from the physical interpretation of reaction coordinates, which is often addressed by correlating physically meaningful parameters with conceptually well-defined but abstract reaction coordinates. Furthermore, machine learning based methods are becoming more and more applicable also to the reaction coordinate problem. This perspective highlights central aspects in the identification and evaluation of reaction coordinates and discusses recent ideas regarding automated computational frameworks to combine the optimization of reaction coordinates and enhanced sampling.