Accuracy of the three-body fragment molecular orbital method applied to Møller-Plesset perturbation theory.
Identifieur interne : 002193 ( PubMed/Curation ); précédent : 002192; suivant : 002194Accuracy of the three-body fragment molecular orbital method applied to Møller-Plesset perturbation theory.
Auteurs : Dmitri G. Fedorov [Japon] ; Kazuya Ishimura [Japon] ; Toyokazu Ishida [Japon] ; Kazuo Kitaura [Japon] ; Peter Pulay [États-Unis] ; Shigeru Nagase [Japon]Source :
- 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
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: Pour aller vers cette notice dans l'étape Curation :002193
Links to Exploration step
pubmed:17330884Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><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 wicri:level="1"><nlm:affiliation>National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan.</nlm:affiliation>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Ishimura, Kazuya" sort="Ishimura, Kazuya" uniqKey="Ishimura K" first="Kazuya" last="Ishimura">Kazuya Ishimura</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Theoretical Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan.</nlm:affiliation>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>Department of Theoretical Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Ishida, Toyokazu" sort="Ishida, Toyokazu" uniqKey="Ishida T" first="Toyokazu" last="Ishida">Toyokazu Ishida</name>
<affiliation wicri:level="1"><nlm:affiliation>National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan.</nlm:affiliation>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Kitaura, Kazuo" sort="Kitaura, Kazuo" uniqKey="Kitaura K" first="Kazuo" last="Kitaura">Kazuo Kitaura</name>
<affiliation wicri:level="1"><nlm:affiliation>National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan.</nlm:affiliation>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Pulay, Peter" sort="Pulay, Peter" uniqKey="Pulay P" first="Peter" last="Pulay">Peter Pulay</name>
<affiliation wicri:level="2"><nlm:affiliation>Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Arkansas</region>
</placeName>
<wicri:cityArea>Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Nagase, Shigeru" sort="Nagase, Shigeru" uniqKey="Nagase S" first="Shigeru" last="Nagase">Shigeru Nagase</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Theoretical Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan.</nlm:affiliation>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>Department of Theoretical Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585</wicri:regionArea>
</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>
<idno type="wicri:Area/PubMed/Curation">002193</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">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 wicri:level="1"><nlm:affiliation>National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan.</nlm:affiliation>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Ishimura, Kazuya" sort="Ishimura, Kazuya" uniqKey="Ishimura K" first="Kazuya" last="Ishimura">Kazuya Ishimura</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Theoretical Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan.</nlm:affiliation>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>Department of Theoretical Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Ishida, Toyokazu" sort="Ishida, Toyokazu" uniqKey="Ishida T" first="Toyokazu" last="Ishida">Toyokazu Ishida</name>
<affiliation wicri:level="1"><nlm:affiliation>National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan.</nlm:affiliation>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Kitaura, Kazuo" sort="Kitaura, Kazuo" uniqKey="Kitaura K" first="Kazuo" last="Kitaura">Kazuo Kitaura</name>
<affiliation wicri:level="1"><nlm:affiliation>National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan.</nlm:affiliation>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Pulay, Peter" sort="Pulay, Peter" uniqKey="Pulay P" first="Peter" last="Pulay">Peter Pulay</name>
<affiliation wicri:level="2"><nlm:affiliation>Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Arkansas</region>
</placeName>
<wicri:cityArea>Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Nagase, Shigeru" sort="Nagase, Shigeru" uniqKey="Nagase S" first="Shigeru" last="Nagase">Shigeru Nagase</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Theoretical Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan.</nlm:affiliation>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>Department of Theoretical Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585</wicri:regionArea>
</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)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/PubMed/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 002193 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Curation/biblio.hfd -nk 002193 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= MersV1 |flux= PubMed |étape= Curation |type= RBID |clé= pubmed:17330884 |texte= Accuracy of the three-body fragment molecular orbital method applied to Møller-Plesset perturbation theory. }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Curation/RBID.i -Sk "pubmed:17330884" \ | HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Curation/biblio.hfd \ | NlmPubMed2Wicri -a MersV1
![]() | This area was generated with Dilib version V0.6.33. | ![]() |