ArticleJournal of chemical theory and computation2014
Comparison between Mean Forces and Swarms-of-Trajectories String Methods.
Article in Journal of chemical theory and computation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
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- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Theoretical Investigation into Polymorphic Transformation between β-HMX and δ-HMX by Finite Temperature String.Molecules (Basel, Switzerland) · 2024Article
- Finite Temperature String with Order Parameter as Collective Variables for Molecular Crystal: A Case of Polymorphic Transformation of TNT under External Electric Field.Molecules (Basel, Switzerland) · 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
- Experimental and Theoretical Investigation of External Electric-Field-Induced Crystallization of TKX-50 from Solution by Finite-Temperature String with Order Parameters as Collective Variables for Ionic Crystals.Molecules (Basel, Switzerland) · 2024Article
- Ligand Lipophilicity Determines Molecular Mechanisms of Nanoparticle Adsorption to Lipid Bilayers.ACS nano · 2024Article
- Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case.Wiley interdisciplinary reviews. Computational molecular science · 2022Article
- A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and Pitfalls.Journal of chemical theory and computation · 2022Article
- Computational methods and theory for ion channel research.Advances in physics: X · 2022Article
- Role of salt-bridging interactions in recognition of viral RNA by arginine-rich peptides.Biophysical journal · 2021Article
- String Method with Swarms-of-Trajectories, Mean Drifts, Lag Time, and Committor.The journal of physical chemistry. A · 2021Article
- Large-Scale Conformational Changes and Protein Function: Breaking theFrontiers in molecular biosciences · 2019Review
- Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbinding.eLife · 2018Article
- Computational membrane biophysics: From ion channel interactions with drugs to cellular function.Biochimica et biophysica acta. Proteins and proteomics · 2017Review
- The Activation of c-Src Tyrosine Kinase: Conformational Transition Pathway and Free Energy Landscape.The journal of physical chemistry. B · 2017Article
- A minimization principle for transition paths of maximum flux for collective variables.Theoretical chemistry accounts · 2017Article
- The allosteric switching mechanism in bacteriophage MS2.The Journal of chemical physics · 2016Article
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.PLoS computational biology · 2016Review
- Extended Phase-Space Methods for Enhanced Sampling in Molecular Simulations: A Review.Frontiers in bioengineering and biotechnology · 2015Review
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The original formulation of the string method in collective variable space is compared with a recent variant called string method with swarms-of-trajectories. The assumptions made in the original method are revisited and the significance of the minimum free energy path (MFEP) is discussed in the context of reactive events. These assumptions are compared to those made in the string method with swarms-of-trajectories, and shown to be equivalent in a certain regime: in particular an expression for the path identified by the swarms-of-trajectories method is given and shown to be closely related to the MFEP. Finally, the algorithmic aspects of both methods are compared.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.