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Accurate and efficient representation of intramolecular energy in ab initio generation of crystal structures. I. Adaptive local approximate models
The global search stage of crystal structure prediction (CSP) methods requires a fine balance between accuracy and computational cost, particularly for the study of large flexible molecules. A major improvement in the accuracy and cost of the intramolecular energy function used in the CrystalPredict...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
International Union of Crystallography
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5134761/ https://www.ncbi.nlm.nih.gov/pubmed/27910837 http://dx.doi.org/10.1107/S2052520616015122 |
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author | Sugden, Isaac Adjiman, Claire S. Pantelides, Constantinos C. |
author_facet | Sugden, Isaac Adjiman, Claire S. Pantelides, Constantinos C. |
author_sort | Sugden, Isaac |
collection | PubMed |
description | The global search stage of crystal structure prediction (CSP) methods requires a fine balance between accuracy and computational cost, particularly for the study of large flexible molecules. A major improvement in the accuracy and cost of the intramolecular energy function used in the CrystalPredictor II [Habgood et al. (2015 ▸). J. Chem. Theory Comput. 11, 1957–1969] program is presented, where the most efficient use of computational effort is ensured via the use of adaptive local approximate model (LAM) placement. The entire search space of the relevant molecule’s conformations is initially evaluated using a coarse, low accuracy grid. Additional LAM points are then placed at appropriate points determined via an automated process, aiming to minimize the computational effort expended in high-energy regions whilst maximizing the accuracy in low-energy regions. As the size, complexity and flexibility of molecules increase, the reduction in computational cost becomes marked. This improvement is illustrated with energy calculations for benzoic acid and the ROY molecule, and a CSP study of molecule (XXVI) from the sixth blind test [Reilly et al. (2016 ▸). Acta Cryst. B72, 439–459], which is challenging due to its size and flexibility. Its known experimental form is successfully predicted as the global minimum. The computational cost of the study is tractable without the need to make unphysical simplifying assumptions. |
format | Online Article Text |
id | pubmed-5134761 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
spelling | pubmed-51347612016-12-05 Accurate and efficient representation of intramolecular energy in ab initio generation of crystal structures. I. Adaptive local approximate models Sugden, Isaac Adjiman, Claire S. Pantelides, Constantinos C. Acta Crystallogr B Struct Sci Cryst Eng Mater Research Papers The global search stage of crystal structure prediction (CSP) methods requires a fine balance between accuracy and computational cost, particularly for the study of large flexible molecules. A major improvement in the accuracy and cost of the intramolecular energy function used in the CrystalPredictor II [Habgood et al. (2015 ▸). J. Chem. Theory Comput. 11, 1957–1969] program is presented, where the most efficient use of computational effort is ensured via the use of adaptive local approximate model (LAM) placement. The entire search space of the relevant molecule’s conformations is initially evaluated using a coarse, low accuracy grid. Additional LAM points are then placed at appropriate points determined via an automated process, aiming to minimize the computational effort expended in high-energy regions whilst maximizing the accuracy in low-energy regions. As the size, complexity and flexibility of molecules increase, the reduction in computational cost becomes marked. This improvement is illustrated with energy calculations for benzoic acid and the ROY molecule, and a CSP study of molecule (XXVI) from the sixth blind test [Reilly et al. (2016 ▸). Acta Cryst. B72, 439–459], which is challenging due to its size and flexibility. Its known experimental form is successfully predicted as the global minimum. The computational cost of the study is tractable without the need to make unphysical simplifying assumptions. International Union of Crystallography 2016-12-01 /pmc/articles/PMC5134761/ /pubmed/27910837 http://dx.doi.org/10.1107/S2052520616015122 Text en © Isaac Sugden et al. 2016 http://creativecommons.org/licenses/by/2.0/uk/ This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited. |
spellingShingle | Research Papers Sugden, Isaac Adjiman, Claire S. Pantelides, Constantinos C. Accurate and efficient representation of intramolecular energy in ab initio generation of crystal structures. I. Adaptive local approximate models |
title | Accurate and efficient representation of intramolecular energy in ab initio generation of crystal structures. I. Adaptive local approximate models |
title_full | Accurate and efficient representation of intramolecular energy in ab initio generation of crystal structures. I. Adaptive local approximate models |
title_fullStr | Accurate and efficient representation of intramolecular energy in ab initio generation of crystal structures. I. Adaptive local approximate models |
title_full_unstemmed | Accurate and efficient representation of intramolecular energy in ab initio generation of crystal structures. I. Adaptive local approximate models |
title_short | Accurate and efficient representation of intramolecular energy in ab initio generation of crystal structures. I. Adaptive local approximate models |
title_sort | accurate and efficient representation of intramolecular energy in ab initio generation of crystal structures. i. adaptive local approximate models |
topic | Research Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5134761/ https://www.ncbi.nlm.nih.gov/pubmed/27910837 http://dx.doi.org/10.1107/S2052520616015122 |
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