A method for determining reaction paths in large molecules: Application to myoglobin

Elber, Ron; Karplus, Martin

doi:10.1016/0009-2614(87)80576-6

Cited by 400 publications

(324 citation statements)

References 14 publications

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“…It is based on a discretised representation of the path originally proposed by Elber and Karplus [57], with modifications to eliminate corner-cutting and sliding-down problems [71], and to improve the stability and convergence properties [75]. Maragakis et al…”

Section: Introductionmentioning

confidence: 99%

A doubly nudged elastic band method for finding transition states

Trygubenko¹,

Wales²

2004

The Journal of Chemical Physics

381

237

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A modification of the nudged elastic band (NEB) method is presented that enables stable optimisations to be run using both the limited-memory quasi-Newton (L-BFGS) and slow-response quenched velocity Verlet (SQVV) minimisers. The performance of this new 'doubly nudged' DNEB method is analysed in conjunction with both minimisers and compared with previous NEB formulations. We find that the fastest DNEB approach (DNEB/L-BFGS) can be quicker by up to two orders of magnitude. Applications to permutational rearrangements of the seven-atom Lennard-Jones cluster (LJ 7 ) and highly cooperative rearrangements of LJ 38 and LJ 75 are presented. We also outline an updated algorithm for constructing complicated multi-step pathways using successive DNEB runs. *

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Section: Introductionmentioning

confidence: 99%

A doubly nudged elastic band method for finding transition states

Trygubenko¹,

Wales²

2004

The Journal of Chemical Physics

381

237

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“…Because of the high dimensionality of the configuration space (ഠ550 000 degrees of freedom), it is highly nontrivial to identify the transition path and the corresponding transition state. We approach this problem with a configuration-space-path technique [11,12] in which the entire transition path is determined simultaneously. In this approach an initial guess for the transition path is relaxed according to the calculated forces until the 3676 0031-9007͞97͞79(19)͞3676 (4) minimum energy path with vanishing forces perpendicular to the path is obtained.…”

Section: (Received 2 July 1997)mentioning

confidence: 99%

Atomistic Determination of Cross-Slip Pathway and Energetics

et al. 1997

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“…15,16 In the present contribution we focus on the doubly 17 -nudged elastic band 18,19 (DNEB) approach.…”

Section: Chain Of State Methodsmentioning

confidence: 99%

Exploring Energy Landscapes: Metrics, Pathways, and Normal-Mode Analysis for Rigid-Body Molecules

Rühle

Kusumaatmaja

Chakrabarti

et al. 2013

J. Chem. Theory Comput.

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We present new methodology for exploring the energy landscapes of molecular systems, using angle-axis variables for the rigid-body rotational coordinates. The key ingredient is a distance measure or metric tensor, which is invariant to global translation and rotation. The metric is used to formulate a generalized nudged elastic band method for calculating pathways, and a full prescription for normal-mode analysis is described. The methodology is tested by mapping the potential energy and free energy landscape of the water octamer, described by the TIP4P potential.

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A method for determining reaction paths in large molecules: Application to myoglobin

Cited by 400 publications

References 14 publications

A doubly nudged elastic band method for finding transition states

A doubly nudged elastic band method for finding transition states

Atomistic Determination of Cross-Slip Pathway and Energetics

Exploring Energy Landscapes: Metrics, Pathways, and Normal-Mode Analysis for Rigid-Body Molecules

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