
Method in a nutshell 


The main problems with finding transition states and pathways using the nudged elastic band (NEB) method are associated with accuracy and efficiency. We have developed a framework for finding transition states that is based on the variable tradeoff between the two, and showed that in most cases the new approach is more than an order of magnitude faster. A short summary of the doubly nudged elastic band approach (DNEB) follows:
We use DNEB method with a revised connection algorithm that is an efficient way of constructing connections between distant minima using multiple DNEB transition state searches. It automatically optimizes transition state candidates from each DNEB run, constructs steepestdescent pathways and analyses the database of minima and transition states to choose which connections need to be established to produce a connected rearrangement pathway. The main features of our revised connection algorithm are as follows:
This work was described in detail in:

Doubly nudged elastic band for a model twodimensional surface. 

Test cases: rearrangements of 38 and 75atom LennardJones clusters  
The doubly nudged elastic band method and connection algorithm were tested on a number of rearrangements of LennardJones clusters. For this purpose we selected rearrangements between the two lowestenergy minima of the LJ_{38} and LJ_{75} clusters. The potential energy surfaces of these are known to have a double funnel morphology and for both clusters the two lowest energy minima are very distinct structurally. The endpoint geometries for each cluster as well as output information are available for download. There are two sets of endpoints for each rearrangement, which correspond to different Euclidean separations. Each set is labeled with value of the separation, which is given in the units of . The endpoints chosen for these tests are not the ones that give the shortest Euclidean distances, even though the paper states so. The geometries of the endpoints and the pathways are in the XYZ format (.xyz files) and can be visualized using the XMakemol program. For each pathway the potential energy as a function of the integrated path length is supplied in .eofs files. Then energy profiles can be plotted using Gnuplot. Alternatively, interactive movies that visualize each rearrangement are available (NB: Macromedia Flash player required. The average size of the movies is 0.8 Mb). This work was described in detail in: S. A. Trygubenko and D. J. Wales, `A Doubly Nudged Elastic Band Method for Finding Transition States', J. Chem. Phys., 120, 20822094 (2004). [JCP Online] [arXiv] Please note that pathways available here are simply the ones that were found with DNEB/Connect algorithm starting from a band obtained with linear interpolation. These pathways are neither the the shortest nor they are the fastest. For the the lowest overall barrier pathway connecting the endpoints for LJ_{38} for a particular choice of the endpoint separation of 3.274 please visit Pathway database website. There you can also find the largest rate contribution pathway connecting the endpoints for LJ_{38} for a particular choice of the endpoint separation of 3.274.



Software  
Calculations were performed using OPTIM program for optimizing geometries and calculating reaction pathways written by D. J. Wales.  
Copyleft 20032006 by Semen Trygubenko
