Vendi sampling for molecular simulations: Diversity as a force for faster convergence and better exploration
Journal article, 2023

Molecular dynamics (MD) is the method of choice for understanding the structure, function, and interactions of molecules. However, MD simulations are limited by the strong metastability of many molecules, which traps them in a single conformation basin for an extended amount of time. Enhanced sampling techniques, such as metadynamics and replica exchange, have been developed to overcome this limitation and accelerate the exploration of complex free energy landscapes. In this paper, we propose Vendi Sampling, a replica-based algorithm for increasing the efficiency and efficacy of the exploration of molecular conformation spaces. In Vendi sampling, replicas are simulated in parallel and coupled via a global statistical measure, the Vendi Score, to enhance diversity. Vendi sampling allows for the recovery of unbiased sampling statistics and dramatically improves sampling efficiency. We demonstrate the effectiveness of Vendi sampling in improving molecular dynamics simulations by showing significant improvements in coverage and mixing between metastable states and convergence of free energy estimates for four common benchmarks, including Alanine Dipeptide and Chignolin.

Author

Amey P. Pasarkar

Princeton University

Gianluca M. Bencomo

Princeton University

Simon Olsson

Chalmers, Computer Science and Engineering (Chalmers), Data Science and AI

Adji Bousso Dieng

Princeton University

Journal of Chemical Physics

0021-9606 (ISSN) 1089-7690 (eISSN)

Vol. 159 14 144108

Subject Categories

Physical Sciences

Chemical Sciences

DOI

10.1063/5.0166172

PubMed

37823459

More information

Latest update

11/17/2023