QM/MM calculations with deMon2k.
Identifieur interne : 002940 ( Main/Exploration ); précédent : 002939; suivant : 002941QM/MM calculations with deMon2k.
Auteurs : Dennis R. Salahub [Canada] ; Sergei Yu Noskov [Canada] ; Bogdan Lev [Australie] ; Rui Zhang [Canada] ; Van Ngo [Canada] ; Annick Goursot [France] ; Patrizia Calaminici [Mexique] ; Andreas M. Köster [Mexique] ; Aurelio Alvarez-Ibarra [Mexique] ; Daniel Mejía-Rodríguez [Mexique] ; Jan Ezá [République tchèque] ; Fabien Cailliez [France] ; Aurélien De La Lande [France]Source :
- Molecules (Basel, Switzerland) [ 1420-3049 ] ; 2015.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Peptides.
- Humans, Models, Molecular, Molecular Dynamics Simulation, Quantum Theory, Software.
Abstract
The density functional code deMon2k employs a fitted density throughout (Auxiliary Density Functional Theory), which offers a great speed advantage without sacrificing necessary accuracy. Powerful Quantum Mechanical/Molecular Mechanical (QM/MM) approaches are reviewed. Following an overview of the basic features of deMon2k that make it efficient while retaining accuracy, three QM/MM implementations are compared and contrasted. In the first, deMon2k is interfaced with the CHARMM MM code (CHARMM-deMon2k); in the second MM is coded directly within the deMon2k software; and in the third the Chemistry in Ruby (Cuby) wrapper is used to drive the calculations. Cuby is also used in the context of constrained-DFT/MM calculations. Each of these implementations is described briefly; pros and cons are discussed and a few recent applications are described briefly. Applications include solvated ions and biomolecules, polyglutamine peptides important in polyQ neurodegenerative diseases, copper monooxygenases and ultra-rapid electron transfer in cryptochromes.
DOI: 10.3390/molecules20034780
PubMed: 25786164
Affiliations:
- Australie, Canada, France, Mexique, République tchèque
- Alberta, Languedoc-Roussillon, Occitanie (région administrative), Île-de-France
- Calgary, Montpellier, Orsay
- Université Paris-Sud, Université de Calgary
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Salahub</name><affiliation wicri:level="4"><nlm:affiliation>Department of Chemistry, CMS-Centre for Molecular Simulation, IQST-Institute for Quantum Science and Technology and ISEEE-Institute for Sustainable Energy, Environment and Economy, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada. dennis.salahub@ucalgary.ca.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Chemistry, CMS-Centre for Molecular Simulation, IQST-Institute for Quantum Science and Technology and ISEEE-Institute for Sustainable Energy, Environment and Economy, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4</wicri:regionArea><orgName type="university">Université de Calgary</orgName><placeName><settlement type="city">Calgary</settlement><region type="state">Alberta</region></placeName></affiliation></author><author><name sortKey="Noskov, Sergei Yu" sort="Noskov, Sergei Yu" uniqKey="Noskov S" first="Sergei Yu" last="Noskov">Sergei Yu Noskov</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biological Science and CMS-Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada. snoskov@ucalgary.ca.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Biological Science and CMS-Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4</wicri:regionArea><orgName type="university">Université de Calgary</orgName><placeName><settlement type="city">Calgary</settlement><region type="state">Alberta</region></placeName></affiliation></author><author><name sortKey="Lev, Bogdan" sort="Lev, Bogdan" uniqKey="Lev B" first="Bogdan" last="Lev">Bogdan Lev</name><affiliation wicri:level="1"><nlm:affiliation>School of Applied Sciences and Health Innovation Research Institute, RMIT University, Melbourne, VIC 3001, Australia. lev.bogdan@gmail.com.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>School of Applied Sciences and Health Innovation Research Institute, RMIT University, Melbourne, VIC 3001</wicri:regionArea><wicri:noRegion>VIC 3001</wicri:noRegion></affiliation></author><author><name sortKey="Zhang, Rui" sort="Zhang, Rui" uniqKey="Zhang R" first="Rui" last="Zhang">Rui Zhang</name><affiliation wicri:level="4"><nlm:affiliation>Department of Chemistry, CMS-Centre for Molecular Simulation, IQST-Institute for Quantum Science and Technology and ISEEE-Institute for Sustainable Energy, Environment and Economy, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada. zhangrui1002@gmail.com.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Chemistry, CMS-Centre for Molecular Simulation, IQST-Institute for Quantum Science and Technology and ISEEE-Institute for Sustainable Energy, Environment and Economy, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4</wicri:regionArea><orgName type="university">Université de Calgary</orgName><placeName><settlement type="city">Calgary</settlement><region type="state">Alberta</region></placeName></affiliation></author><author><name sortKey="Ngo, Van" sort="Ngo, Van" uniqKey="Ngo V" first="Van" last="Ngo">Van Ngo</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biological Science and CMS-Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada. nvan.ucalgary@gmail.com.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Biological Science and CMS-Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4</wicri:regionArea><orgName type="university">Université de Calgary</orgName><placeName><settlement type="city">Calgary</settlement><region type="state">Alberta</region></placeName></affiliation></author><author><name sortKey="Goursot, Annick" sort="Goursot, Annick" uniqKey="Goursot A" first="Annick" last="Goursot">Annick Goursot</name><affiliation wicri:level="1"><nlm:affiliation>Institut Charles Gerhardt, UMR 5253 CNRS/UM2/ENSCM/UM1, 8 rue de l'Ecole Normale, Montpellier 34296, France. annick.goursot@gmail.com.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institut Charles Gerhardt, UMR 5253 CNRS/UM2/ENSCM/UM1, 8 rue de l'Ecole Normale, Montpellier 34296</wicri:regionArea><wicri:noRegion>34296</wicri:noRegion><placeName><settlement type="city">Montpellier</settlement><region type="region" nuts="2">Occitanie (région administrative)</region><region type="old region" nuts="2">Languedoc-Roussillon</region></placeName></affiliation></author><author><name sortKey="Calaminici, Patrizia" sort="Calaminici, Patrizia" uniqKey="Calaminici P" first="Patrizia" last="Calaminici">Patrizia Calaminici</name><affiliation wicri:level="1"><nlm:affiliation>Departamento de Química, CINVESTAV, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, México D.F. 07000, Mexico. pcalamin@cinvestav.mx.</nlm:affiliation><country xml:lang="fr">Mexique</country><wicri:regionArea>Departamento de Química, CINVESTAV, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, México D.F. 07000</wicri:regionArea><wicri:noRegion>México D.F. 07000</wicri:noRegion></affiliation></author><author><name sortKey="Koster, Andreas M" sort="Koster, Andreas M" uniqKey="Koster A" first="Andreas M" last="Köster">Andreas M. Köster</name><affiliation wicri:level="1"><nlm:affiliation>Departamento de Química, CINVESTAV, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, México D.F. 07000, Mexico. akoster@cinvestav.mx.</nlm:affiliation><country xml:lang="fr">Mexique</country><wicri:regionArea>Departamento de Química, CINVESTAV, Centro de Investigación y de Estudios Avanzados, Av. 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Instituto Politécnico Nacional, 2508, A.P. 14-740, México D.F. 07000</wicri:regionArea><wicri:noRegion>México D.F. 07000</wicri:noRegion></affiliation></author><author><name sortKey=" Eza, Jan" sort=" Eza, Jan" uniqKey=" Eza J" first="Jan" last=" Ezá">Jan Ezá</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Organic Chemistry and Biochemistry and Gilead Science and IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6 166 10, Czech Republic. rezac@uochb.cas.cz.</nlm:affiliation><country xml:lang="fr">République tchèque</country><wicri:regionArea>Institute of Organic Chemistry and Biochemistry and Gilead Science and IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6 166 10</wicri:regionArea><wicri:noRegion>Prague 6 166 10</wicri:noRegion></affiliation></author><author><name sortKey="Cailliez, Fabien" sort="Cailliez, Fabien" uniqKey="Cailliez F" first="Fabien" last="Cailliez">Fabien Cailliez</name><affiliation wicri:level="4"><nlm:affiliation>Laboratoire de Chimie Physique-CNRS UMR 8000, Université Paris-Sud, Bật. 349, Campus d'Orsay. 15, rue Jean Perrin, Orsay Cedex 91405, France. fabien.cailliez@u-psud.fr.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire de Chimie Physique-CNRS UMR 8000, Université Paris-Sud, Bật. 349, Campus d'Orsay. 15, rue Jean Perrin, Orsay Cedex 91405</wicri:regionArea><wicri:noRegion>91405</wicri:noRegion><orgName type="university">Université Paris-Sud</orgName><placeName><settlement type="city">Orsay</settlement><region type="region" nuts="2">Île-de-France</region></placeName></affiliation></author><author><name sortKey="De La Lande, Aurelien" sort="De La Lande, Aurelien" uniqKey="De La Lande A" first="Aurélien" last="De La Lande">Aurélien De La Lande</name><affiliation wicri:level="4"><nlm:affiliation>Laboratoire de Chimie Physique-CNRS UMR 8000, Université Paris-Sud, Bật. 349, Campus d'Orsay. 15, rue Jean Perrin, Orsay Cedex 91405, France. aurelien.de-la-lande@u-psud.fr.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire de Chimie Physique-CNRS UMR 8000, Université Paris-Sud, Bật. 349, Campus d'Orsay. 15, rue Jean Perrin, Orsay Cedex 91405</wicri:regionArea><wicri:noRegion>91405</wicri:noRegion><orgName type="university">Université Paris-Sud</orgName><placeName><settlement type="city">Orsay</settlement><region type="region" nuts="2">Île-de-France</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:25786164</idno><idno type="pmid">25786164</idno><idno type="doi">10.3390/molecules20034780</idno><idno type="wicri:Area/PubMed/Corpus">002F22</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002F22</idno><idno type="wicri:Area/PubMed/Curation">002E44</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002E44</idno><idno type="wicri:Area/PubMed/Checkpoint">002E44</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">002E44</idno><idno type="wicri:Area/Ncbi/Merge">002358</idno><idno type="wicri:Area/Ncbi/Curation">002358</idno><idno type="wicri:Area/Ncbi/Checkpoint">002358</idno><idno type="wicri:Area/Main/Merge">002940</idno><idno type="wicri:Area/Main/Curation">002940</idno><idno type="wicri:Area/Main/Exploration">002940</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">QM/MM calculations with deMon2k.</title><author><name sortKey="Salahub, Dennis R" sort="Salahub, Dennis R" uniqKey="Salahub D" first="Dennis R" last="Salahub">Dennis R. Salahub</name><affiliation wicri:level="4"><nlm:affiliation>Department of Chemistry, CMS-Centre for Molecular Simulation, IQST-Institute for Quantum Science and Technology and ISEEE-Institute for Sustainable Energy, Environment and Economy, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada. dennis.salahub@ucalgary.ca.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Chemistry, CMS-Centre for Molecular Simulation, IQST-Institute for Quantum Science and Technology and ISEEE-Institute for Sustainable Energy, Environment and Economy, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4</wicri:regionArea><orgName type="university">Université de Calgary</orgName><placeName><settlement type="city">Calgary</settlement><region type="state">Alberta</region></placeName></affiliation></author><author><name sortKey="Noskov, Sergei Yu" sort="Noskov, Sergei Yu" uniqKey="Noskov S" first="Sergei Yu" last="Noskov">Sergei Yu Noskov</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biological Science and CMS-Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada. snoskov@ucalgary.ca.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Biological Science and CMS-Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4</wicri:regionArea><orgName type="university">Université de Calgary</orgName><placeName><settlement type="city">Calgary</settlement><region type="state">Alberta</region></placeName></affiliation></author><author><name sortKey="Lev, Bogdan" sort="Lev, Bogdan" uniqKey="Lev B" first="Bogdan" last="Lev">Bogdan Lev</name><affiliation wicri:level="1"><nlm:affiliation>School of Applied Sciences and Health Innovation Research Institute, RMIT University, Melbourne, VIC 3001, Australia. lev.bogdan@gmail.com.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>School of Applied Sciences and Health Innovation Research Institute, RMIT University, Melbourne, VIC 3001</wicri:regionArea><wicri:noRegion>VIC 3001</wicri:noRegion></affiliation></author><author><name sortKey="Zhang, Rui" sort="Zhang, Rui" uniqKey="Zhang R" first="Rui" last="Zhang">Rui Zhang</name><affiliation wicri:level="4"><nlm:affiliation>Department of Chemistry, CMS-Centre for Molecular Simulation, IQST-Institute for Quantum Science and Technology and ISEEE-Institute for Sustainable Energy, Environment and Economy, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada. zhangrui1002@gmail.com.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Chemistry, CMS-Centre for Molecular Simulation, IQST-Institute for Quantum Science and Technology and ISEEE-Institute for Sustainable Energy, Environment and Economy, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4</wicri:regionArea><orgName type="university">Université de Calgary</orgName><placeName><settlement type="city">Calgary</settlement><region type="state">Alberta</region></placeName></affiliation></author><author><name sortKey="Ngo, Van" sort="Ngo, Van" uniqKey="Ngo V" first="Van" last="Ngo">Van Ngo</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biological Science and CMS-Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada. nvan.ucalgary@gmail.com.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Biological Science and CMS-Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4</wicri:regionArea><orgName type="university">Université de Calgary</orgName><placeName><settlement type="city">Calgary</settlement><region type="state">Alberta</region></placeName></affiliation></author><author><name sortKey="Goursot, Annick" sort="Goursot, Annick" uniqKey="Goursot A" first="Annick" last="Goursot">Annick Goursot</name><affiliation wicri:level="1"><nlm:affiliation>Institut Charles Gerhardt, UMR 5253 CNRS/UM2/ENSCM/UM1, 8 rue de l'Ecole Normale, Montpellier 34296, France. annick.goursot@gmail.com.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institut Charles Gerhardt, UMR 5253 CNRS/UM2/ENSCM/UM1, 8 rue de l'Ecole Normale, Montpellier 34296</wicri:regionArea><wicri:noRegion>34296</wicri:noRegion><placeName><settlement type="city">Montpellier</settlement><region type="region" nuts="2">Occitanie (région administrative)</region><region type="old region" nuts="2">Languedoc-Roussillon</region></placeName></affiliation></author><author><name sortKey="Calaminici, Patrizia" sort="Calaminici, Patrizia" uniqKey="Calaminici P" first="Patrizia" last="Calaminici">Patrizia Calaminici</name><affiliation wicri:level="1"><nlm:affiliation>Departamento de Química, CINVESTAV, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, México D.F. 07000, Mexico. pcalamin@cinvestav.mx.</nlm:affiliation><country xml:lang="fr">Mexique</country><wicri:regionArea>Departamento de Química, CINVESTAV, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, México D.F. 07000</wicri:regionArea><wicri:noRegion>México D.F. 07000</wicri:noRegion></affiliation></author><author><name sortKey="Koster, Andreas M" sort="Koster, Andreas M" uniqKey="Koster A" first="Andreas M" last="Köster">Andreas M. Köster</name><affiliation wicri:level="1"><nlm:affiliation>Departamento de Química, CINVESTAV, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, México D.F. 07000, Mexico. akoster@cinvestav.mx.</nlm:affiliation><country xml:lang="fr">Mexique</country><wicri:regionArea>Departamento de Química, CINVESTAV, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, México D.F. 07000</wicri:regionArea><wicri:noRegion>México D.F. 07000</wicri:noRegion></affiliation></author><author><name sortKey="Alvarez Ibarra, Aurelio" sort="Alvarez Ibarra, Aurelio" uniqKey="Alvarez Ibarra A" first="Aurelio" last="Alvarez-Ibarra">Aurelio Alvarez-Ibarra</name><affiliation wicri:level="1"><nlm:affiliation>Departamento de Química, CINVESTAV, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, México D.F. 07000, Mexico. aalvarezi@cinvestav.mx.</nlm:affiliation><country xml:lang="fr">Mexique</country><wicri:regionArea>Departamento de Química, CINVESTAV, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, México D.F. 07000</wicri:regionArea><wicri:noRegion>México D.F. 07000</wicri:noRegion></affiliation></author><author><name sortKey="Mejia Rodriguez, Daniel" sort="Mejia Rodriguez, Daniel" uniqKey="Mejia Rodriguez D" first="Daniel" last="Mejía-Rodríguez">Daniel Mejía-Rodríguez</name><affiliation wicri:level="1"><nlm:affiliation>Departamento de Química, CINVESTAV, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, México D.F. 07000, Mexico. dmejia@cinvestav.mx.</nlm:affiliation><country xml:lang="fr">Mexique</country><wicri:regionArea>Departamento de Química, CINVESTAV, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, México D.F. 07000</wicri:regionArea><wicri:noRegion>México D.F. 07000</wicri:noRegion></affiliation></author><author><name sortKey=" Eza, Jan" sort=" Eza, Jan" uniqKey=" Eza J" first="Jan" last=" Ezá">Jan Ezá</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Organic Chemistry and Biochemistry and Gilead Science and IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6 166 10, Czech Republic. rezac@uochb.cas.cz.</nlm:affiliation><country xml:lang="fr">République tchèque</country><wicri:regionArea>Institute of Organic Chemistry and Biochemistry and Gilead Science and IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6 166 10</wicri:regionArea><wicri:noRegion>Prague 6 166 10</wicri:noRegion></affiliation></author><author><name sortKey="Cailliez, Fabien" sort="Cailliez, Fabien" uniqKey="Cailliez F" first="Fabien" last="Cailliez">Fabien Cailliez</name><affiliation wicri:level="4"><nlm:affiliation>Laboratoire de Chimie Physique-CNRS UMR 8000, Université Paris-Sud, Bật. 349, Campus d'Orsay. 15, rue Jean Perrin, Orsay Cedex 91405, France. fabien.cailliez@u-psud.fr.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire de Chimie Physique-CNRS UMR 8000, Université Paris-Sud, Bật. 349, Campus d'Orsay. 15, rue Jean Perrin, Orsay Cedex 91405</wicri:regionArea><wicri:noRegion>91405</wicri:noRegion><orgName type="university">Université Paris-Sud</orgName><placeName><settlement type="city">Orsay</settlement><region type="region" nuts="2">Île-de-France</region></placeName></affiliation></author><author><name sortKey="De La Lande, Aurelien" sort="De La Lande, Aurelien" uniqKey="De La Lande A" first="Aurélien" last="De La Lande">Aurélien De La Lande</name><affiliation wicri:level="4"><nlm:affiliation>Laboratoire de Chimie Physique-CNRS UMR 8000, Université Paris-Sud, Bật. 349, Campus d'Orsay. 15, rue Jean Perrin, Orsay Cedex 91405, France. aurelien.de-la-lande@u-psud.fr.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire de Chimie Physique-CNRS UMR 8000, Université Paris-Sud, Bật. 349, Campus d'Orsay. 15, rue Jean Perrin, Orsay Cedex 91405</wicri:regionArea><wicri:noRegion>91405</wicri:noRegion><orgName type="university">Université Paris-Sud</orgName><placeName><settlement type="city">Orsay</settlement><region type="region" nuts="2">Île-de-France</region></placeName></affiliation></author></analytic><series><title level="j">Molecules (Basel, Switzerland)</title><idno type="eISSN">1420-3049</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Humans</term><term>Models, Molecular</term><term>Molecular Dynamics Simulation</term><term>Peptides (chemistry)</term><term>Quantum Theory</term><term>Software</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Humains</term><term>Logiciel</term><term>Modèles moléculaires</term><term>Peptides ()</term><term>Simulation de dynamique moléculaire</term><term>Théorie quantique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Peptides</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Humans</term><term>Models, Molecular</term><term>Molecular Dynamics Simulation</term><term>Quantum Theory</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Humains</term><term>Logiciel</term><term>Modèles moléculaires</term><term>Peptides</term><term>Simulation de dynamique moléculaire</term><term>Théorie quantique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The density functional code deMon2k employs a fitted density throughout (Auxiliary Density Functional Theory), which offers a great speed advantage without sacrificing necessary accuracy. Powerful Quantum Mechanical/Molecular Mechanical (QM/MM) approaches are reviewed. Following an overview of the basic features of deMon2k that make it efficient while retaining accuracy, three QM/MM implementations are compared and contrasted. In the first, deMon2k is interfaced with the CHARMM MM code (CHARMM-deMon2k); in the second MM is coded directly within the deMon2k software; and in the third the Chemistry in Ruby (Cuby) wrapper is used to drive the calculations. Cuby is also used in the context of constrained-DFT/MM calculations. Each of these implementations is described briefly; pros and cons are discussed and a few recent applications are described briefly. Applications include solvated ions and biomolecules, polyglutamine peptides important in polyQ neurodegenerative diseases, copper monooxygenases and ultra-rapid electron transfer in cryptochromes.</div></front></TEI><affiliations><list><country><li>Australie</li><li>Canada</li><li>France</li><li>Mexique</li><li>République tchèque</li></country><region><li>Alberta</li><li>Languedoc-Roussillon</li><li>Occitanie (région administrative)</li><li>Île-de-France</li></region><settlement><li>Calgary</li><li>Montpellier</li><li>Orsay</li></settlement><orgName><li>Université Paris-Sud</li><li>Université de Calgary</li></orgName></list><tree><country name="Canada"><region name="Alberta"><name sortKey="Salahub, Dennis R" sort="Salahub, Dennis R" uniqKey="Salahub D" first="Dennis R" last="Salahub">Dennis R. Salahub</name></region><name sortKey="Ngo, Van" sort="Ngo, Van" uniqKey="Ngo V" first="Van" last="Ngo">Van Ngo</name><name sortKey="Noskov, Sergei Yu" sort="Noskov, Sergei Yu" uniqKey="Noskov S" first="Sergei Yu" last="Noskov">Sergei Yu Noskov</name><name sortKey="Zhang, Rui" sort="Zhang, Rui" uniqKey="Zhang R" first="Rui" last="Zhang">Rui Zhang</name></country><country name="Australie"><noRegion><name sortKey="Lev, Bogdan" sort="Lev, Bogdan" uniqKey="Lev B" first="Bogdan" last="Lev">Bogdan Lev</name></noRegion></country><country name="France"><region name="Occitanie (région administrative)"><name sortKey="Goursot, Annick" sort="Goursot, Annick" uniqKey="Goursot A" first="Annick" last="Goursot">Annick Goursot</name></region><name sortKey="Cailliez, Fabien" sort="Cailliez, Fabien" uniqKey="Cailliez F" first="Fabien" last="Cailliez">Fabien Cailliez</name><name sortKey="De La Lande, Aurelien" sort="De La Lande, Aurelien" uniqKey="De La Lande A" first="Aurélien" last="De La Lande">Aurélien De La Lande</name></country><country name="Mexique"><noRegion><name sortKey="Calaminici, Patrizia" sort="Calaminici, Patrizia" uniqKey="Calaminici P" first="Patrizia" last="Calaminici">Patrizia Calaminici</name></noRegion><name sortKey="Alvarez Ibarra, Aurelio" sort="Alvarez Ibarra, Aurelio" uniqKey="Alvarez Ibarra A" first="Aurelio" last="Alvarez-Ibarra">Aurelio Alvarez-Ibarra</name><name sortKey="Koster, Andreas M" sort="Koster, Andreas M" uniqKey="Koster A" first="Andreas M" last="Köster">Andreas M. Köster</name><name sortKey="Mejia Rodriguez, Daniel" sort="Mejia Rodriguez, Daniel" uniqKey="Mejia Rodriguez D" first="Daniel" last="Mejía-Rodríguez">Daniel Mejía-Rodríguez</name></country><country name="République tchèque"><noRegion><name sortKey=" Eza, Jan" sort=" Eza, Jan" uniqKey=" Eza J" first="Jan" last=" Ezá">Jan Ezá</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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