Nudged-elastic-band algorithm

Crehuet, R., Thomas, A., Field, M.J. An implementation of the nudged elastic band algorithm and application to the reaction mechanism of HGXPRTase from Plasmodium falciparum, J. Mol. Graph. Model. 2005,24,102-10. 

Implementation of the Nudged Elastic Band Algorithm and AppUcation to the Reaction Mechanism of HGXPRTase from Plasmodium Falciparum. 

This is an identical equation for the minimum energy path [9,10] or the so-called steepest descent path. The first implementation of an algorithm to compute minimum energy paths based on the above formula was the LUP (Locally Updated Planes) method [9] that did not include the constraint on the displacement size. This is formally correct since different parameterizations of the path are possible, but may lead to numerical problems in which the distances between the intermediates grow without control. This was adjusted to produce more stable algorithms by the Nudge Elastic Band approach [11] and later by the String method [10]. 

Keywords Ab initio molecular dynamics simulations Always stable predictor-corrector algorithm Associated liquids Basis set Bom-Oppenheimer molecular dynamics simulations Car-Parrinello molecular dynamics simulations Catalysis Collective variable Discrete variable representation Dispersion Effective core potential Enhanced sampling Fictitious mass First-principles molecular dynamics simulations Free energy surface Hartree-Fock exchange Ionic liquids Linear scaling Metadynamics Nudged elastic band Numerically tabulated atom-centered orbitals Plane waves Pseudopotential Rare event Relativistic electronic structure Retention potential Self consistent field SHAKE algorithm ... 

Generate an initial guess for the path connecting the initial and final coordinates of the system using an MEP algorithm, such as self-penalty walk (SPW) or nudged-elastic band. ... 

The first two present new approaches the seam space nudged elastic band method (SS-NEB) and the double Newton-Raphson algorithm using composed steps (DNR-CS). The third report describes an automated search method to find minimum energy CIXs, the so-called SMF/ ADDF approach. 

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