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A growing string method for the reaction pathway defined by a Newton trajectory
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10.1063/1.1885467
/content/aip/journal/jcp/122/17/10.1063/1.1885467
http://aip.metastore.ingenta.com/content/aip/journal/jcp/122/17/10.1063/1.1885467

Figures

Image of FIG. 1.
FIG. 1.

GS method on Müller–Brown potential from minimum to minimum . The predictor step at is shown, and the corrector back to the searched RP (arrows). The desired number of nodes is . The Newton trajectory to the initial direction is included for comparison. The growing string follows the NT very well.

Image of FIG. 2.
FIG. 2.

Reaction path on the Müller–Brown potential from minimum to minimum . An 11-nodechain is obtained using the Newton projector. The convergence of the growing string method needs the calculation of 19 gradients. The search direction for the GS method is readjusted on the course.

Image of FIG. 3.
FIG. 3.

Effort of the growing ends string method for the MB potential.

Image of FIG. 4.
FIG. 4.

Newton trajectory (dashes) and the growing ends string method (connected bullets) for a four-well potential including an initial chain, for comparison. (a) The fixed search direction between both minima is not well chosen; for the second part of the RP, see text. (b) The search direction for the GS method is readjusted on the course.

Image of FIG. 5.
FIG. 5.

Growing ends string method with 23 nodes for the potential (assuming argon). Shown is the energy profile. The left arrows indicate the two outmost right atoms which are mainly involved in the rearrangement. From top to bottom, the resulting curves for the corrector thresholds , 0.5, and 0.1 are shown. The SP at node 11 is well approximated.

Image of FIG. 6.
FIG. 6.

Two Newton trajectories for a four-well potential with minima C5 and . Thin long dashes: NT to search direction between both minima. (It is not well chosen.) Short bold dashes: The search direction for the NT is well adapted to connect the C5 and minima.

Image of FIG. 7.
FIG. 7.

Approximation of Newton trajectories for alanine dipeptide between the C5 and minima, see text. Method: projected and inverse gradient [Eq. (9)] dampened by . The search direction for the NT is the direction from start to finish, and after three steps the corresponding direction from former chain points to finish. Shown is the energy profile in a.u. (a) , , maximal 55 steps per node. (b) and is so small that 151 steps per node are used. (c) NT between the two SPs, , and for the upper, as well as for the lower curve, maximal 151 steps per node.

Image of FIG. 8.
FIG. 8.

Convergence history for curve (b) of Fig. 7 for the norm of the projected gradient. In the inlay, curves of nodes 2 to 23 count from top to bottom.

Image of FIG. 9.
FIG. 9.

Approximation of Newton trajectories for alanine dipeptide between the minima and C5, see text. Method: modified CG+ optimization. The search direction for the NT is the direction from start to finish, and after three steps the direction from former chain points to finish. The energy profile is shown in a.u. The lower curve is for (max 134 steps per node: which were used throughout) and the upper one is for . The energies of the SPs and of the intermediate minimum are included.

Image of FIG. 10.
FIG. 10.

Approximation of Newton trajectories for alanine dipeptide between the minima and C5, see text. Methods: projected and inverse gradient (thin points) starting at C5, and modified CG+ optimization (thick bullets) starting at . The two coordinates of the 60D internal coordinates are shown in a Ramachandran diagram, with adapted axes to the searched reaction patway. The projected gradient paths correspond with the profiles (a), (b), and the lower curve of (c) of Fig. 7. The connected bold points correspond with the CG+ results of Fig. 9. The “better” one (more left and below) is for ; it is the lower curve of Fig. 9. The other chain of points belongs to . The two SPs (*) and the intermediate minimum (+) are included.

Image of FIG. 11.
FIG. 11.

Approximation of two NTs for alanine dipeptide between the C5 minimum and intermediate minimum, , and from there to the minimum , as well. Method: modified CG+ optimization. Two coordinates are shown in a Ramachandran diagram. Ten nodes are used for every string, and thresholds and 0.003 33, respectively. The inlay shows the energy profile of both paths in the order of their calculation.

Image of FIG. 12.
FIG. 12.

Approximation of four NTs for alanine dipeptide between the C5 minimum and . Method: modified CG+ optimization. The linear combinations of coordinate are used for predictor steps, and five nodes are calculated for every string. The thresholds are , 0.007 5, 0.01, and 0.02 from bottom to top.

Tables

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Scheme 2 SP search in GAUSSIAN03 by Berny’s method.

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Scheme 3 Shell script for an cluster: Calculation of NTs

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Scheme 4 Head of GAUSSIAN03 input for corrector steps (file oben).

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Scheme 5 Shell script for the alanine dipeptide molecule: Calculation of NTs

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/content/aip/journal/jcp/122/17/10.1063/1.1885467
2005-05-03
2014-04-20
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: A growing string method for the reaction pathway defined by a Newton trajectory
http://aip.metastore.ingenta.com/content/aip/journal/jcp/122/17/10.1063/1.1885467
10.1063/1.1885467
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