title: Fep1d: a script for the analysis of reaction coordinates.
abstract: The dynamics of complex systems with many degrees of freedom can be analyzed by projecting it onto one or few coordinates (collective variables). The dynamics is often described then as diffusion on a free energy landscape associated with the coordinates. Fep1d is a script for the analysis of such one-dimensional coordinates. The script allows one to construct conventional and cut-based free energy profiles, to assess the optimality of a reaction coordinate, to inspect whether the dynamics projected on the coordinate is diffusive, to transform (rescale) the reaction coordinate to more convenient ones, and to compute such quantities as the mean first passage time, the transition path times, the coordinate dependent diffusion coefficient, and so forth. Here, we describe the implemented functionality together with the underlying theoretical framework.
authors.affiliation: Astbury Center for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom.
authors.forename: Polina V
authors.initials: PV
authors.lastname: Banushkina
authors.forename: Sergei V
authors.initials: SV
authors.lastname: Krivov
mesh_terms: D003198:Computer Simulation; D017510:Protein Folding; D013816:Thermodynamics
keywords: cut free energy profile; diffusion; dimesionality reduction; free energy profile; reaction coordinate