TY - JOUR
T1 - Accelerating Molecular Dynamics through Informed Resetting
AU - Church, Jonathan R.
AU - Blumer, Ofir
AU - Keidar, Tommer D.
AU - Ploutno, Leo
AU - Reuveni, Shlomi
AU - Hirshberg, Barak
N1 - Publisher Copyright:
© 2025 The Authors. Published by American Chemical Society.
PY - 2025/1/28
Y1 - 2025/1/28
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85214326691&partnerID=8YFLogxK
U2 - 10.1021/acs.jctc.4c01238
DO - 10.1021/acs.jctc.4c01238
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C2 - 39772645
AN - SCOPUS:85214326691
SN - 1549-9618
VL - 21
SP - 605
EP - 613
JO - Journal of Chemical Theory and Computation
JF - Journal of Chemical Theory and Computation
IS - 2
ER -