TY - JOUR
T1 - Highly parallelizable path sampling with minimal rejections using asynchronous replica exchange and infinite swaps
AU - Zhang, Daniel T.
AU - Baldauf, Lukas
AU - Roet, Sander
AU - Lervik, Anders
AU - van Erp, Titus S.
N1 - Publisher Copyright:
© 2024 the Author(s). Published by PNAS.
PY - 2024/2/13
Y1 - 2024/2/13
N2 - Capturing rare yet pivotal events poses a significant challenge for molecular simulations. Path sampling provides a unique approach to tackle this issue without altering the potential energy landscape or dynamics, enabling recovery of both thermodynamic and kinetic information. However, despite its exponential acceleration compared to standard molecular dynamics, generating numerous trajectories can still require a long time. By harnessing our recent algorithmic innovations—particularly subtrajectory moves with high acceptance, coupled with asynchronous replica exchange featuring infinite swaps—we establish a highly parallelizable and rapidly converging path sampling protocol, compatible with diverse high-performance computing architectures. We demonstrate our approach on the liquid–vapor phase transition in superheated water, the unfolding of the chignolin protein, and water dissociation. The latter, performed at the ab initio level, achieves comparable statistical accuracy within days, in contrast to a previous study requiring over a year.
AB - Capturing rare yet pivotal events poses a significant challenge for molecular simulations. Path sampling provides a unique approach to tackle this issue without altering the potential energy landscape or dynamics, enabling recovery of both thermodynamic and kinetic information. However, despite its exponential acceleration compared to standard molecular dynamics, generating numerous trajectories can still require a long time. By harnessing our recent algorithmic innovations—particularly subtrajectory moves with high acceptance, coupled with asynchronous replica exchange featuring infinite swaps—we establish a highly parallelizable and rapidly converging path sampling protocol, compatible with diverse high-performance computing architectures. We demonstrate our approach on the liquid–vapor phase transition in superheated water, the unfolding of the chignolin protein, and water dissociation. The latter, performed at the ab initio level, achieves comparable statistical accuracy within days, in contrast to a previous study requiring over a year.
KW - Markov-chain Monte Carlo
KW - asynchronous replica exchange
KW - infinite swapping
KW - path sampling
KW - rare events
UR - http://www.scopus.com/inward/record.url?scp=85185096243&partnerID=8YFLogxK
U2 - 10.1073/pnas.2318731121
DO - 10.1073/pnas.2318731121
M3 - Article
SN - 0027-8424
VL - 121
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
IS - 7
M1 - e2318731121
ER -