Accuracy of the three-body fragment molecular orbital method applied to Møller-Plesset perturbation theory.
Identifieur interne : 002193 ( PubMed/Corpus ); précédent : 002192; suivant : 002194Accuracy of the three-body fragment molecular orbital method applied to Møller-Plesset perturbation theory.
Auteurs : Dmitri G. Fedorov ; Kazuya Ishimura ; Toyokazu Ishida ; Kazuo Kitaura ; Peter Pulay ; Shigeru NagaseSource :
- Journal of computational chemistry [ 0192-8651 ] ; 2007.
Abstract
The three-body energy expansion in the fragment molecular orbital method (FMO) was applied to the 2nd order Møller-Plesset theory (MP2). The accuracy of both the two and three-body expansions was determined for water clusters, alanine n-mers (alpha-helices and beta-strands) and one synthetic protein, using the 6-31G* and 6-311G* basis sets. At the best level of theory (three-body, two molecules/residues per fragment), the absolute errors in energy relative to ab initio MP2 were at most 1.2 and 5.0 mhartree, for the 6-31G* and 6-311G* basis sets, respectively. The relative accuracy was at worst 99.996% and 99.96%, for 6-31G* and 6-311G*, respectively. A three-body approximation was introduced and the optimum threshold value was determined. The protein calculation (6-31G*) at the production level (FMO2/2) took 3 h on 36 3.2-GHz Pentium 4 nodes and had the absolute error in the MP2 correlation energy of only 2 kcal/mol.
DOI: 10.1002/jcc.20645
PubMed: 17330884
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Fedorov</name><affiliation><nlm:affiliation>National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan.</nlm:affiliation></affiliation></author><author><name sortKey="Ishimura, Kazuya" sort="Ishimura, Kazuya" uniqKey="Ishimura K" first="Kazuya" last="Ishimura">Kazuya Ishimura</name><affiliation><nlm:affiliation>Department of Theoretical Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan.</nlm:affiliation></affiliation></author><author><name sortKey="Ishida, Toyokazu" sort="Ishida, Toyokazu" uniqKey="Ishida T" first="Toyokazu" last="Ishida">Toyokazu Ishida</name><affiliation><nlm:affiliation>National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan.</nlm:affiliation></affiliation></author><author><name sortKey="Kitaura, Kazuo" sort="Kitaura, Kazuo" uniqKey="Kitaura K" first="Kazuo" last="Kitaura">Kazuo Kitaura</name><affiliation><nlm:affiliation>National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan.</nlm:affiliation></affiliation></author><author><name sortKey="Pulay, Peter" sort="Pulay, Peter" uniqKey="Pulay P" first="Peter" last="Pulay">Peter Pulay</name><affiliation><nlm:affiliation>Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701.</nlm:affiliation></affiliation></author><author><name sortKey="Nagase, Shigeru" sort="Nagase, Shigeru" uniqKey="Nagase S" first="Shigeru" last="Nagase">Shigeru Nagase</name><affiliation><nlm:affiliation>Department of Theoretical Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2007">2007</date><idno type="RBID">pubmed:17330884</idno><idno type="pmid">17330884</idno><idno type="doi">10.1002/jcc.20645</idno><idno type="wicri:Area/PubMed/Corpus">002193</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002193</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Accuracy of the three-body fragment molecular orbital method applied to Møller-Plesset perturbation theory.</title><author><name sortKey="Fedorov, Dmitri G" sort="Fedorov, Dmitri G" uniqKey="Fedorov D" first="Dmitri G" last="Fedorov">Dmitri G. Fedorov</name><affiliation><nlm:affiliation>National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan.</nlm:affiliation></affiliation></author><author><name sortKey="Ishimura, Kazuya" sort="Ishimura, Kazuya" uniqKey="Ishimura K" first="Kazuya" last="Ishimura">Kazuya Ishimura</name><affiliation><nlm:affiliation>Department of Theoretical Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan.</nlm:affiliation></affiliation></author><author><name sortKey="Ishida, Toyokazu" sort="Ishida, Toyokazu" uniqKey="Ishida T" first="Toyokazu" last="Ishida">Toyokazu Ishida</name><affiliation><nlm:affiliation>National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan.</nlm:affiliation></affiliation></author><author><name sortKey="Kitaura, Kazuo" sort="Kitaura, Kazuo" uniqKey="Kitaura K" first="Kazuo" last="Kitaura">Kazuo Kitaura</name><affiliation><nlm:affiliation>National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan.</nlm:affiliation></affiliation></author><author><name sortKey="Pulay, Peter" sort="Pulay, Peter" uniqKey="Pulay P" first="Peter" last="Pulay">Peter Pulay</name><affiliation><nlm:affiliation>Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701.</nlm:affiliation></affiliation></author><author><name sortKey="Nagase, Shigeru" sort="Nagase, Shigeru" uniqKey="Nagase S" first="Shigeru" last="Nagase">Shigeru Nagase</name><affiliation><nlm:affiliation>Department of Theoretical Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Journal of computational chemistry</title><idno type="ISSN">0192-8651</idno><imprint><date when="2007" type="published">2007</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The three-body energy expansion in the fragment molecular orbital method (FMO) was applied to the 2nd order Møller-Plesset theory (MP2). The accuracy of both the two and three-body expansions was determined for water clusters, alanine n-mers (alpha-helices and beta-strands) and one synthetic protein, using the 6-31G* and 6-311G* basis sets. At the best level of theory (three-body, two molecules/residues per fragment), the absolute errors in energy relative to ab initio MP2 were at most 1.2 and 5.0 mhartree, for the 6-31G* and 6-311G* basis sets, respectively. The relative accuracy was at worst 99.996% and 99.96%, for 6-31G* and 6-311G*, respectively. A three-body approximation was introduced and the optimum threshold value was determined. The protein calculation (6-31G*) at the production level (FMO2/2) took 3 h on 36 3.2-GHz Pentium 4 nodes and had the absolute error in the MP2 correlation energy of only 2 kcal/mol.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">17330884</PMID><DateCompleted><Year>2007</Year><Month>06</Month><Day>25</Day></DateCompleted><DateRevised><Year>2018</Year><Month>02</Month><Day>07</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0192-8651</ISSN><JournalIssue CitedMedium="Print"><Volume>28</Volume><Issue>9</Issue><PubDate><Year>2007</Year><Month>Jul</Month><Day>15</Day></PubDate></JournalIssue><Title>Journal of computational chemistry</Title><ISOAbbreviation>J Comput Chem</ISOAbbreviation></Journal><ArticleTitle>Accuracy of the three-body fragment molecular orbital method applied to Møller-Plesset perturbation theory.</ArticleTitle><Pagination><MedlinePgn>1476-1484</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1002/jcc.20645</ELocationID><Abstract><AbstractText>The three-body energy expansion in the fragment molecular orbital method (FMO) was applied to the 2nd order Møller-Plesset theory (MP2). The accuracy of both the two and three-body expansions was determined for water clusters, alanine n-mers (alpha-helices and beta-strands) and one synthetic protein, using the 6-31G* and 6-311G* basis sets. At the best level of theory (three-body, two molecules/residues per fragment), the absolute errors in energy relative to ab initio MP2 were at most 1.2 and 5.0 mhartree, for the 6-31G* and 6-311G* basis sets, respectively. The relative accuracy was at worst 99.996% and 99.96%, for 6-31G* and 6-311G*, respectively. A three-body approximation was introduced and the optimum threshold value was determined. The protein calculation (6-31G*) at the production level (FMO2/2) took 3 h on 36 3.2-GHz Pentium 4 nodes and had the absolute error in the MP2 correlation energy of only 2 kcal/mol.</AbstractText><CopyrightInformation>Copyright (c) 2007 Wiley Periodicals, Inc.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Fedorov</LastName><ForeName>Dmitri G</ForeName><Initials>DG</Initials><AffiliationInfo><Affiliation>National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ishimura</LastName><ForeName>Kazuya</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Theoretical Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ishida</LastName><ForeName>Toyokazu</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kitaura</LastName><ForeName>Kazuo</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pulay</LastName><ForeName>Peter</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nagase</LastName><ForeName>Shigeru</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Theoretical Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Comput Chem</MedlineTA><NlmUniqueID>9878362</NlmUniqueID><ISSNLinking>0192-8651</ISSNLinking></MedlineJournalInfo></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2007</Year><Month>3</Month><Day>3</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2007</Year><Month>3</Month><Day>3</Day><Hour>9</Hour><Minute>1</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2007</Year><Month>3</Month><Day>3</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">17330884</ArticleId><ArticleId IdType="doi">10.1002/jcc.20645</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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