title: Spectral gap optimization of order parameters for sampling complex molecular systems.
abstract: In modern-day simulations of many-body systems, much of the computational complexity is shifted to the identification of slowly changing molecular order parameters called collective variables (CVs) or reaction coordinates. A vast array of enhanced-sampling methods are based on the identification and biasing of these low-dimensional order parameters, whose fluctuations are important in driving rare events of interest. Here, we describe a new algorithm for finding optimal low-dimensional CVs for use in enhanced-sampling biasing methods like umbrella sampling, metadynamics, and related methods, when limited prior static and dynamic information is known about the system, and a much larger set of candidate CVs is specified. The algorithm involves estimating the best combination of these candidate CVs, as quantified by a maximum path entropy estimate of the spectral gap for dynamics viewed as a function of that CV. The algorithm is called spectral gap optimization of order parameters (SGOOP). Through multiple practical examples, we show how this postprocessing procedure can lead to optimization of CV and several orders of magnitude improvement in the convergence of the free energy calculated through metadynamics, essentially giving the ability to extract useful information even from unsuccessful metadynamics runs.
authors.affiliation: Department of Chemistry, Columbia University, New York, NY 10027.
authors.forename: Pratyush
authors.initials: P
authors.lastname: Tiwary
authors.affiliation: Department of Chemistry, Columbia University, New York, NY 10027 bb8@columbia.edu.
authors.forename: B J
authors.initials: BJ
authors.lastname: Berne
mesh_terms: D000465:Algorithms; D019277:Entropy; D008958:Models, Molecular; D008962:Models, Theoretical; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry
chemical_list: D010455:Peptides
keywords: caliber; collective variables; enhanced sampling; spectral gap; timescale separation