Accelerating Molecular Dynamics through Informed Resetting

Jonathan R. Church, Ofir Blumer, Tommer D. Keidar, Leo Ploutno, Shlomi Reuveni, Barak Hirshberg*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

We present a procedure for enhanced sampling of molecular dynamics simulations through informed stochastic resetting. Many phenomena, such as protein folding and crystal nucleation, occur over time scales inaccessible in standard simulations. We recently showed that stochastic resetting can accelerate molecular simulations that exhibit broad transition time distributions. However, standard stochastic resetting does not exploit any information about the reaction progress. For a model system and chignolin in explicit water, we demonstrate that an informed resetting protocol leads to greater accelerations than standard stochastic resetting in molecular dynamics and Metadynamics simulations. This is achieved by resetting only when a certain condition is met, e.g., when the distance from the target along the reaction coordinate is larger than some threshold. We use these accelerated simulations to infer important kinetic observables such as the unbiased mean first-passage time and direct transit time. For the latter, Metadynamics with informed resetting leads to speedups of 2-3 orders of magnitude over unbiased simulations with relative errors of only ∼35-70%. Our work significantly extends the applicability of stochastic resetting for enhanced sampling of molecular simulations.

Original languageEnglish
Pages (from-to)605-613
Number of pages9
JournalJournal of Chemical Theory and Computation
Volume21
Issue number2
DOIs
StatePublished - 28 Jan 2025

Fingerprint

Dive into the research topics of 'Accelerating Molecular Dynamics through Informed Resetting'. Together they form a unique fingerprint.

Cite this