Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field

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 CH...

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Detalles Bibliográficos
Autores principales: Ferraro, Marta Beatriz, Facelli, Julio César
Publicado: 2009
Materias:
Crystal structure prediction
Force fields
GAFF
Genetic algorithms
AMBER force-field
Cluster prediction
Computer program
Distributed Computing
Flexible molecules
Local energy
Modified genetic algorithms
Parallel genetic algorithms
Standard force field
Clustering algorithms
Computer science
Molecules
Parallel algorithms
Crystal structure
algorithm
article
computer simulation
crystallization
genetics
Algorithms
Computer Simulation
Crystallization
Genetics
Acceso en línea:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_01928651_v30_n13_p1973_Seonah
http://hdl.handle.net/20.500.12110/paper_01928651_v30_n13_p1973_Seonah
Aporte de:
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires
id paper:paper_01928651_v30_n13_p1973_Seonah
record_format dspace
spelling paper:paper_01928651_v30_n13_p1973_Seonah2023-06-08T15:19:59Z Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field Ferraro, Marta Beatriz Facelli, Julio César 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 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. Fil:Ferraro, M.B. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Facelli, J.C. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. 2009 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_01928651_v30_n13_p1973_Seonah http://hdl.handle.net/20.500.12110/paper_01928651_v30_n13_p1973_Seonah
institution Universidad de Buenos Aires
institution_str I-28
repository_str R-134
collection Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic 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
spellingShingle 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
Ferraro, Marta Beatriz
Facelli, Julio César
Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field
topic_facet 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
description 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.
author Ferraro, Marta Beatriz
Facelli, Julio César
author_facet Ferraro, Marta Beatriz
Facelli, Julio César
author_sort Ferraro, Marta Beatriz
title Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field
title_short Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field
title_full Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field
title_fullStr Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field
title_full_unstemmed Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field
title_sort crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field
publishDate 2009
url https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_01928651_v30_n13_p1973_Seonah
http://hdl.handle.net/20.500.12110/paper_01928651_v30_n13_p1973_Seonah
work_keys_str_mv AT ferraromartabeatriz crystalstructurepredictionofflexiblemoleculesusingparallelgeneticalgorithmswithastandardforcefield
AT facellijuliocesar crystalstructurepredictionofflexiblemoleculesusingparallelgeneticalgorithmswithastandardforcefield
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