Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field |
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| Authors: | Seonah Kim Anita M Orendt Marta B Ferraro Julio C Facelli |
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| Institution: | 1. Center for High Performance Computing, University of Utah, 155 South 1452 East Room 405, Salt Lake City, Utah 84112–0190;2. Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. I (1428), Buenos Aires, Argentina;3. Department of Biomedical Informatics, University of Utah, 155 South 1452 East Room 405, Salt Lake City, Utah 84112–0190 |
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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. J Comput Chem, 2009 |
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| Keywords: | crystal structure prediction genetic algorithms force fields GAFF |
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