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Optimization of a genetic algorithm for searching molecular conformer space
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10.1063/1.3656323
/content/aip/journal/jcp/135/17/10.1063/1.3656323
http://aip.metastore.ingenta.com/content/aip/journal/jcp/135/17/10.1063/1.3656323

Figures

Image of FIG. 1.
FIG. 1.

The five molecules used to optimize GA parameters. Rotated bonds are indicated by bold lines.

Image of FIG. 2.
FIG. 2.

GA efficiency for the DAWMOE molecule on (a) HF/6-31G rigid, (b) relaxed, and (c) SCRF surfaces as a function of population size and mutation rate for parameter sets located by the meta-GA. Unreliable parameter sets are shown as hollow squares. Results for all molecules are included in the supplementary material (Ref. 37).

Image of FIG. 3.
FIG. 3.

Regions corresponding to good GA parameter sets (dark grey), high mutation rate (dots) and unreliable regions (diagonal stripes). Parameter sets in the remaining unshaded region are reliable but inefficient.

Image of FIG. 4.
FIG. 4.

GA efficiency vs. selection method and crossover method for the molecule DAWMOE on the HF/6-31G relaxed surface with population size and mutation rate held constant at values indicated in the text. Results for all molecules are included in the supplementary material (Ref. 37).

Image of FIG. 5.
FIG. 5.

GA efficiency vs. crossover method and crossover probability for the molecule DAWMOE on the HF/6-31G relaxed surface with population size and mutation rate held constant at values indicated in the text. Results for all molecules are included in the supplementary material (Ref. 37).

Image of FIG. 6.
FIG. 6.

Three conformers of the FABPUU molecule: (a) The CSD reference structure, reoptimized. (b) The false minimum. (c) The pseudo-C 3 global minimum. Δ E (mEh), relative to the proposed minimum, (c) is indicated below each structure.

Image of FIG. 7.
FIG. 7.

Energy (Hartree) of best conformer by GA generation for 5 independent GA runs on the relaxed FABPUU molecule using HF/6-31g. Between generations 450 and 700, several lines are coincident. The generation size is 10.

Tables

Generic image for table
Table I.

Genome defninition of the Meta-GA.

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Table II.

Mean, minimum and maximum population sizes and mutation rates for the 10 best genetic algorithms found for each molecule and model chemistry combination. The mean population size and mutation rate is also shown for each model chemistry.

Generic image for table
Table III.

GA performance on larger molecules. Molecule names in small caps indicate structure key names from the CSD Database. N indicates the number of rotatable bonds in each molecule; x, y indicate bonds restricted to 2-way, 3-way rotation respectively, E represents the energy of the minimum structure in Hartree (target energy, see text for further details), N gen is the generation in which the global minimum was located in each run.

Generic image for table
Table IV.

Distribution of conformer energies, expressed as ΔE (mEh) w.r.t. the energy of the proposed global minimum, E = −1075.473674. N eval is the number of non-zero molecule energies evaluated in the GA instance.

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/content/aip/journal/jcp/135/17/10.1063/1.3656323
2011-11-02
2014-04-24
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Optimization of a genetic algorithm for searching molecular conformer space
http://aip.metastore.ingenta.com/content/aip/journal/jcp/135/17/10.1063/1.3656323
10.1063/1.3656323
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