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Abstract:

This article describes the application of our distributed computing framework for crystal structure prediction (CSP) the modified genetic algorithms for crystal and cluster prediction (MGAC), to predict the crystal structure of flexible molecules using the general Amber force field (GAFF) and the CHARMM program. The MGAC distributed computing framework includes a series of tightly integrated computer programs for generating the molecule's force field, sampling crystal structures using a distributed parallel genetic algorithm and local energy minimization of the structures followed by the classifying, sorting, and archiving of the most relevant structures. Our results indicate that the method can consistently find the experimentally known crystal structures of flexible molecules, but the number of missing structures and poor ranking observed in some crystals show the need for further improvement of the potential. © 2009 Wiley Periodicals, Inc.

Registro:

Documento: Artículo
Título:Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field
Autor:Seonah, K.; Orendt, A.M.; Ferraro, M.B.; Facelli, J.C.
Filiación:Center for High Performance Computing, University of Utah, 155 South 1452 East, Salt Lake City, UT 84112-0190, United States
Departamento de Física, Facultad de Ciencias Exactas y Naturales, Ciudad Universitaria, Pab. 1 (1428), Buenos Aires, Argentina
Department of Biomedical Informatics, University of Utah, 155 South 1452 East, Salt Lake City, UT 84112-0190, United States
Palabras clave:Crystal structure prediction; Force fields; GAFF; Genetic algorithms; AMBER force-field; Cluster prediction; Computer program; Crystal structure prediction; Distributed Computing; Flexible molecules; Force fields; GAFF; Local energy; Modified genetic algorithms; Parallel genetic algorithms; Standard force field; Clustering algorithms; Computer science; Genetic algorithms; Molecules; Parallel algorithms; Crystal structure; algorithm; article; computer simulation; crystallization; genetics; Algorithms; Computer Simulation; Crystallization; Genetics
Año:2009
Volumen:30
Número:13
Página de inicio:1973
Página de fin:1985
DOI: http://dx.doi.org/10.1002/jcc.21189
Título revista:Journal of Computational Chemistry
Título revista abreviado:J. Comput. Chem.
ISSN:01928651
CODEN:JCCHD
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_01928651_v30_n13_p1973_Seonah

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Citas:

---------- APA ----------
Seonah, K., Orendt, A.M., Ferraro, M.B. & Facelli, J.C. (2009) . Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field. Journal of Computational Chemistry, 30(13), 1973-1985.
http://dx.doi.org/10.1002/jcc.21189
---------- CHICAGO ----------
Seonah, K., Orendt, A.M., Ferraro, M.B., Facelli, J.C. "Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field" . Journal of Computational Chemistry 30, no. 13 (2009) : 1973-1985.
http://dx.doi.org/10.1002/jcc.21189
---------- MLA ----------
Seonah, K., Orendt, A.M., Ferraro, M.B., Facelli, J.C. "Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field" . Journal of Computational Chemistry, vol. 30, no. 13, 2009, pp. 1973-1985.
http://dx.doi.org/10.1002/jcc.21189
---------- VANCOUVER ----------
Seonah, K., Orendt, A.M., Ferraro, M.B., Facelli, J.C. Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field. J. Comput. Chem. 2009;30(13):1973-1985.
http://dx.doi.org/10.1002/jcc.21189