Literature DB >> 17546677

Improving the efficiency of the NEB reaction path finding algorithm.

Ignacio Fdez Galván1, Martin J Field.   

Abstract

The nudged elastic band (NEB) method is a successful optimization method for obtaining minimum energy reaction paths if only the initial and final structures are known. However, the original implementation of the method had some limitations, which has meant that there has been considerable interest in proposing alternative NEB formulations, which show improved convergence behavior. In this work, we present two modifications to the standard NEB procedure. The first involves the use of a second-order quasi-Newton optimization technique applied separately to each of the images that form the path. The second consists of the use of an interpolating spline to represent the path. This ensures that the images along the path are evenly spaced and means that the arbitrary spring forces employed in the standard NEB method are no longer necessary. We tested these modifications on a set of small, but relatively complex, chemical systems and found that the computation time was reduced by as much as 90% compared with the standard method.

Mesh:

Year:  2008        PMID: 17546677     DOI: 10.1002/jcc.20780

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  4 in total

1.  Negative Impact of Carbapenem Methylation on the Reactivity of β-Lactams for Cysteine Acylation as Revealed by Quantum Calculations and Kinetic Analyses.

Authors:  Nicholus Bhattacharjee; Sébastien Triboulet; Michel Arthur; Catherine M Bougault; Vincent Dubée; Matthieu Fonvielle; Zainab Edoo; Jean-Emmanuel Hugonnet; Mélanie Ethève-Quelquejeu; Jean-Pierre Simorre; Martin J Field
Journal:  Antimicrob Agents Chemother       Date:  2019-03-27       Impact factor: 5.191

2.  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

3.  PyCPR - a python-based implementation of the Conjugate Peak Refinement (CPR) algorithm for finding transition state structures.

Authors:  Florian J Gisdon; Martin Culka; G Matthias Ullmann
Journal:  J Mol Model       Date:  2016-09-20       Impact factor: 1.810

4.  Conformational Transition Pathways of Epidermal Growth Factor Receptor Kinase Domain from Multiple Molecular Dynamics Simulations and Bayesian Clustering.

Authors:  Yan Li; Xiang Li; Weiya Ma; Zigang Dong
Journal:  J Chem Theory Comput       Date:  2014-06-18       Impact factor: 6.006

  4 in total

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