ArticleJournal of chemical theory and computation2022
A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and Pitfalls.
Article in Journal of chemical theory and computation, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
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- Free-Energy Landscapes of HBV Hexamer Closure Reveal Key Structural Features of the Transition.Journal of chemical theory and computation · 2026Article
- Following the Committor Flow: A Data-Driven Discovery of Transition Pathways.Journal of chemical theory and computation · 2026Article
- Advanced Computational Methods in Protein Simulations: A Case Study of Enhanced Sampling Applied to Membrane Transporters.Advances in experimental medicine and biology · 2026Review
- Data-driven enhanced sampling of mechanistic pathways.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Probing Passive Permeation of Tetracycline: Are Simulations Ready for beyond-Rule-of-Five Drug Permeability Calculation?The journal of physical chemistry. B · 2025Article
- The String Method with Swarms of Trajectories: A Tutorial for Free-Energy Calculations Along a Zero-Drift Pathway.The journal of physical chemistry. B · 2025Article
- Article
- Expanded Functionality and Portability for the Colvars Library.The journal of physical chemistry. B · 2024Article
- Deciphering the Interdomain Coupling in a Gram-Negative Bacterial Membrane Insertase.The journal of physical chemistry. B · 2024Article
- A weak coupling mechanism for the early steps of the recovery stroke of myosin VI: A free energy simulation and string method analysis.PLoS computational biology · 2024Article
- Elucidating molecular mechanisms of protoxin-II state-specific binding to the human NaV1.7 channel.The Journal of general physiology · 2024Article
- Improved Sampling of Adaptive Path Collective Variables by Stabilized Extended-System Dynamics.Journal of chemical theory and computation · 2023Article
- Molecular Free Energies, Rates, and Mechanisms from Data-Efficient Path Sampling Simulations.Journal of chemical theory and computation · 2023Article
- Chasing collective variables using temporal data-driven strategies.QRB discovery · 2023Article
- Perspective: Path Sampling Methods Applied to Enzymatic Catalysis.Journal of chemical theory and computation · 2022Review
- An investigation of the YidC-mediated membrane insertion of Pf3 coat protein using molecular dynamics simulations.Frontiers in molecular biosciences · 2022Article
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Authors and funding
8 authors.
Funding
Abstract
The string method with swarms of trajectories (SMwST) is an algorithm that identifies a physically meaningful transition pathway─a one-dimensional curve, embedded within a high-dimensional space of selected collective variables. The SMwST algorithm leans on a series of short, unbiased molecular dynamics simulations spawned at different locations of the discretized path, from whence an average dynamic drift is determined to evolve the string toward an optimal pathway. However conceptually simple in both its theoretical formulation and practical implementation, the SMwST algorithm is computationally intensive and requires a careful choice of parameters for optimal cost-effectiveness in applications to challenging problems in chemistry and biology. In this contribution, the SMwST algorithm is presented in a self-contained manner, discussing with a critical eye its theoretical underpinnings, applicability, inherent limitations, and use in the context of path-following free-energy calculations and their possible extension to kinetics modeling. Through multiple simulations of a prototypical polypeptide, combining the search of the transition pathway and the computation of the potential of mean force along it, several practical aspects of the methodology are examined with the objective of optimizing the computational effort, yet without sacrificing accuracy. In light of the results reported here, we propose some general guidelines aimed at improving the efficiency and reliability of the computed pathways and free-energy profiles underlying the conformational transitions at hand.
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Registered trials
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