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Journal of Chemical Physics / Volume 135 / Issue 17 / ARTICLES / Theoretical Methods and Algorithms

J. Chem. Phys. 135, 174106 (2011); http://dx.doi.org/10.1063/1.3656323 (10 pages)

Optimization of a genetic algorithm for searching molecular conformer space

Zoe E. Brain1 and Matthew A. Addicoat2

1Department of Computer Science, Australian National University, Canberra, ACT 0200, Australia
2Research School of Chemistry and Department of Computer Science, Australian National University, Canberra, ACT 0200, Australia

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(Received 25 August 2011; accepted 7 October 2011; published online 2 November 2011)

We present two sets of tunings that are broadly applicable to conformer searches of isolated molecules using a genetic algorithm (GA). In order to find the most efficient tunings for the GA, a second GA – a meta-genetic algorithm – was used to tune the first genetic algorithm to reliably find the already known a priori correct answer with minimum computational resources. It is shown that these tunings are appropriate for a variety of molecules with different characteristics, and most importantly that the tunings are independent of the underlying model chemistry but that the tunings for rigid and relaxed surfaces differ slightly. It is shown that for the problem of molecular conformational search, the most efficient GA actually reduces to an evolutionary algorithm.

© 2011 American Institute of Physics

Article Outline

  1. INTRODUCTION
  2. COMPUTATIONAL DETAILS
    1. Determination of optimum GA parameters
    2. Restart mechanisms
    3. Molecular calculations
  3. RESULTS AND DISCUSSION
    1. Effect of selection method
    2. Effect of crossover method
    3. Application to larger molecules
    4. Convergence behaviour
    5. Applicability
  4. CONCLUSIONS

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KEYWORDS and PACS

Keywords

genetic algorithms, HF calculations, molecular configurations

PACS

  • 31.15.xr

    Self-consistent-field methods

  • 33.15.Bh

    General molecular conformation and symmetry; stereochemistry

ARTICLE DATA

Digital Object Identifier
http://dx.doi.org/10.1063/1.3656323

PUBLICATION DATA

ISSN

0021-9606 (print)  
1089-7690 (online)

Publisher

$abstract.society.value is a Member of CrossRef American Institute of Physics

For access to fully linked references, you need to log in.
    C. Baysal and H. Meirovitch, J. Chem. Phys. 105, 7868 (1996)JCPSA6000105000017007868000001.

    C. D. Maranas and C. A. Floudas, J. Chem. Phys. 100, 1247 (1994)JCPSA6000100000002001247000001.


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