Literature DB >> 15268346

A doubly nudged elastic band method for finding transition states.

Semen A Trygubenko1, David J Wales.   

Abstract

A modification of the nudged elastic band (NEB) method is presented that enables stable optimizations to be run using both the limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) quasi-Newton and slow-response quenched velocity Verlet minimizers. The performance of this new "doubly nudged" DNEB method is analyzed in conjunction with both minimizers and compared with previous NEB formulations. We find that the fastest DNEB approach (DNEB/L-BFGS) can be quicker by up to 2 orders of magnitude. Applications to permutational rearrangements of the seven-atom Lennard-Jones cluster (LJ7) and highly cooperative rearrangements of LJ38 and LJ75 are presented. We also outline an updated algorithm for constructing complicated multi-step pathways using successive DNEB runs. Copyright 2004 American Institute of Physics

Entities:  

Year:  2004        PMID: 15268346     DOI: 10.1063/1.1636455

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  24 in total

1.  Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin.

Authors:  Bin W Zhang; David Jasnow; Daniel M Zuckerman
Journal:  Proc Natl Acad Sci U S A       Date:  2007-11-01       Impact factor: 11.205

2.  Exploration of effective potential landscapes using coarse reverse integration.

Authors:  Thomas A Frewen; Gerhard Hummer; Ioannis G Kevrekidis
Journal:  J Chem Phys       Date:  2009-10-07       Impact factor: 3.488

3.  RNA Modeling with the Computational Energy Landscape Framework.

Authors:  Konstantin Röder; Samuela Pasquali
Journal:  Methods Mol Biol       Date:  2021

4.  Kudi: A free open-source python library for the analysis of properties along reaction paths.

Authors:  Stefan Vogt-Geisse
Journal:  J Mol Model       Date:  2016-04-23       Impact factor: 1.810

5.  Archetypal landscapes for deep neural networks.

Authors:  Philipp C Verpoort; Alpha A Lee; David J Wales
Journal:  Proc Natl Acad Sci U S A       Date:  2020-08-25       Impact factor: 11.205

6.  POLARIS: Path of Least Action Analysis on Energy Landscapes.

Authors:  Evan Seitz; Joachim Frank
Journal:  J Chem Inf Model       Date:  2020-02-20       Impact factor: 4.956

7.  Characterization of hydrogen bonding motifs in proteins: hydrogen elimination monitoring by ultraviolet photodissociation mass spectrometry.

Authors:  Lindsay J Morrison; Wenrui Chai; Jake A Rosenberg; Graeme Henkelman; Jennifer S Brodbelt
Journal:  Phys Chem Chem Phys       Date:  2017-08-02       Impact factor: 3.676

8.  Comparison of Three Chain-of-States Methods: Nudged Elastic Band and Replica Path with Restraints or Constraints.

Authors:  Peng Tao; Milan Hodošček; Joseph D Larkin; Yihan Shao; Bernard R Brooks
Journal:  J Chem Theory Comput       Date:  2012-09-27       Impact factor: 6.006

9.  The energy landscape, folding pathways and the kinetics of a knotted protein.

Authors:  Michael C Prentiss; David J Wales; Peter G Wolynes
Journal:  PLoS Comput Biol       Date:  2010-07-01       Impact factor: 4.475

Review 10.  Towards operando computational modeling in heterogeneous catalysis.

Authors:  Lukáš Grajciar; Christopher J Heard; Anton A Bondarenko; Mikhail V Polynski; Jittima Meeprasert; Evgeny A Pidko; Petr Nachtigall
Journal:  Chem Soc Rev       Date:  2018-11-12       Impact factor: 54.564

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