Applying Grid Computing to the Parameter Sweep of a Group Difference Pseudopotential
Identifieur interne : 000497 ( Istex/Corpus ); précédent : 000496; suivant : 000498Applying Grid Computing to the Parameter Sweep of a Group Difference Pseudopotential
Auteurs : Wibke Sudholt ; K. Baldridge ; David Abramson ; Colin Enticott ; Slavisa GaricSource :
- Lecture Notes in Computer Science [ 0302-9743 ] ; 2004.
Abstract
Abstract: Theoretical modeling of chemical and biological processes is a key to understand nature and to predict experiments. Unfortunately, this is very data and computation extensive. However, the worldwide computing grid can now provide the necessary resources. Here, we present a coupling of the GAMESS quantum chemical code to the Nimrod/G grid distribution tool, which is applied to the parameter scan of a group difference pseudopotential (GDP). This represents the initial step in parameterization of a capping atom for hybrid quantum mechanics-molecular mechanics (QM/MM) calculations. The results give hints to the physical forces of functional group distinctions and starting points for later parameter optimizations. The demonstrated technology significantly extends the manageability of accurate, but costly quantum chemical calculations and is valuable for many applications involving thousands of independent runs.
Url:
DOI: 10.1007/978-3-540-24685-5_19
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Unfortunately, this is very data and computation extensive. However, the worldwide computing grid can now provide the necessary resources. Here, we present a coupling of the GAMESS quantum chemical code to the Nimrod/G grid distribution tool, which is applied to the parameter scan of a group difference pseudopotential (GDP). This represents the initial step in parameterization of a capping atom for hybrid quantum mechanics-molecular mechanics (QM/MM) calculations. The results give hints to the physical forces of functional group distinctions and starting points for later parameter optimizations. 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type="first">Colin</forename><surname>Enticott</surname></persName><email>Colin.Enticott@csse.monash.edu.au</email><affiliation>Center for Enterprise Distributed Systems (DSTC) and School of Computer Science and Software Engineering, Monash University, 3800, Clayton, Victoria, Australia</affiliation></author><author xml:id="author-5"><persName><forename type="first">Slavisa</forename><surname>Garic</surname></persName><email>Slavisa.Garic@infotech.monash.edu.au</email><affiliation>Center for Enterprise Distributed Systems (DSTC) and School of Computer Science and Software Engineering, Monash University, 3800, Clayton, Victoria, Australia</affiliation></author></analytic><monogr><title level="m">Computational Science - ICCS 2004</title><title level="m" type="sub">4th International Conference, Kraków, Poland, June 6-9, 2004, Proceedings, Part I</title><idno type="pISBN">978-3-540-22114-2</idno><idno type="eISBN">978-3-540-24685-5</idno><idno type="pISSN">0302-9743</idno><idno 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Unfortunately, this is very data and computation extensive. However, the worldwide computing grid can now provide the necessary resources. Here, we present a coupling of the GAMESS quantum chemical code to the Nimrod/G grid distribution tool, which is applied to the parameter scan of a group difference pseudopotential (GDP). This represents the initial step in parameterization of a capping atom for hybrid quantum mechanics-molecular mechanics (QM/MM) calculations. The results give hints to the physical forces of functional group distinctions and starting points for later parameter optimizations. The demonstrated technology significantly extends the manageability of accurate, but costly quantum chemical calculations and is valuable for many applications involving thousands of independent runs.</p></abstract><textClass><keywords scheme="Book-Subject-Collection"><list><label>SUCO11645</label><item><term>Computer Science</term></item></list></keywords></textClass><textClass><keywords scheme="Book-Subject-Group"><list><label>I</label><label>I14002</label><label>I16005</label><label>I17001</label><label>I18008</label><label>I21009</label><label>M1400X</label><item><term>Computer Science</term></item><item><term>Software Engineering/Programming and Operating Systems</term></item><item><term>Theory of Computation</term></item><item><term>Mathematics of Computing</term></item><item><term>Information Systems and Communication Service</term></item><item><term>Computing Methodologies</term></item><item><term>Computational Mathematics and Numerical 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403</Street><Postcode>1098 SJ</Postcode><City>Amsterdam</City><Country>The Netherlands</Country></OrgAddress></Affiliation><Affiliation ID="Aff17"><OrgDivision>Faculty of Sciences, Section of Computational Science</OrgDivision><OrgName>University of Amsterdam</OrgName><OrgAddress><Street>Kruislaan 403</Street><Postcode>1098 SJ</Postcode><City>Amsterdam</City><Country>The Netherlands</Country></OrgAddress></Affiliation><Affiliation ID="Aff18"><OrgDivision>Computer Science Department</OrgDivision><OrgName>University of Tennessee</OrgName><OrgAddress><Postcode>TN 37996-3450</Postcode><City>Knoxville</City><Country>USA</Country></OrgAddress></Affiliation></EditorGroup></BookHeader><Part ID="Part2"><PartInfo TocLevels="0"><PartID>2</PartID><PartSequenceNumber>2</PartSequenceNumber><PartTitle>Track on Grid Computing</PartTitle><PartChapterCount>18</PartChapterCount><PartContext><SeriesID>558</SeriesID><BookTitle>Computational Science - ICCS 2004</BookTitle></PartContext></PartInfo><Chapter ID="Chap19" Language="En"><ChapterInfo ChapterType="OriginalPaper" ContainsESM="No" NumberingDepth="2" NumberingStyle="ContentOnly" TocLevels="0"><ChapterID>19</ChapterID><ChapterDOI>10.1007/978-3-540-24685-5_19</ChapterDOI><ChapterSequenceNumber>19</ChapterSequenceNumber><ChapterTitle Language="En">Applying Grid Computing to the Parameter Sweep of a Group Difference Pseudopotential</ChapterTitle><ChapterFirstPage>148</ChapterFirstPage><ChapterLastPage>155</ChapterLastPage><ChapterCopyright><CopyrightHolderName>Springer-Verlag Berlin Heidelberg</CopyrightHolderName><CopyrightYear>2004</CopyrightYear></ChapterCopyright><ChapterGrants Type="Regular"><MetadataGrant Grant="OpenAccess"></MetadataGrant><AbstractGrant Grant="OpenAccess"></AbstractGrant><BodyPDFGrant Grant="Restricted"></BodyPDFGrant><BodyHTMLGrant Grant="Restricted"></BodyHTMLGrant><BibliographyGrant Grant="Restricted"></BibliographyGrant><ESMGrant Grant="Restricted"></ESMGrant></ChapterGrants><ChapterContext><SeriesID>558</SeriesID><PartID>2</PartID><BookID>978-3-540-24685-5</BookID><BookTitle>Computational Science - ICCS 2004</BookTitle></ChapterContext></ChapterInfo><ChapterHeader><AuthorGroup><Author AffiliationIDS="Aff19"><AuthorName DisplayOrder="Western"><GivenName>Wibke</GivenName><FamilyName>Sudholt</FamilyName></AuthorName><Contact><Email>wibke@sdsc.edu</Email></Contact></Author><Author AffiliationIDS="Aff19"><AuthorName DisplayOrder="Western"><GivenName>Kim</GivenName><GivenName>K.</GivenName><FamilyName>Baldridge</FamilyName></AuthorName><Contact><Email>kimb@sdsc.edu</Email></Contact></Author><Author AffiliationIDS="Aff20"><AuthorName DisplayOrder="Western"><GivenName>David</GivenName><FamilyName>Abramson</FamilyName></AuthorName><Contact><Email>davida@csse.monash.edu.au</Email></Contact></Author><Author AffiliationIDS="Aff20"><AuthorName DisplayOrder="Western"><GivenName>Colin</GivenName><FamilyName>Enticott</FamilyName></AuthorName><Contact><Email>Colin.Enticott@csse.monash.edu.au</Email></Contact></Author><Author AffiliationIDS="Aff20"><AuthorName DisplayOrder="Western"><GivenName>Slavisa</GivenName><FamilyName>Garic</FamilyName></AuthorName><Contact><Email>Slavisa.Garic@infotech.monash.edu.au</Email></Contact></Author><Affiliation ID="Aff19"><OrgDivision>Department of Chemistry & Biochemistry and San Diego Supercomputer Center (SDSC)</OrgDivision><OrgName>University of California, San Diego (UCSD)</OrgName><OrgAddress><Street>9500 Gilman Dr</Street><City>La Jolla</City><State>CA</State><Postcode>92093-0505</Postcode><Country>USA</Country></OrgAddress></Affiliation><Affiliation ID="Aff20"><OrgDivision>Center for Enterprise Distributed Systems (DSTC) and School of Computer Science and Software Engineering</OrgDivision><OrgName>Monash University</OrgName><OrgAddress><City>Clayton</City><State>Victoria</State><Postcode>3800</Postcode><Country>Australia</Country></OrgAddress></Affiliation></AuthorGroup><Abstract ID="Abs1" Language="En"><Heading>Abstract</Heading><Para>Theoretical modeling of chemical and biological processes is a key to understand nature and to predict experiments. Unfortunately, this is very data and computation extensive. However, the worldwide computing grid can now provide the necessary resources. Here, we present a coupling of the GAMESS quantum chemical code to the Nimrod/G grid distribution tool, which is applied to the parameter scan of a group difference pseudopotential (GDP). This represents the initial step in parameterization of a capping atom for hybrid quantum mechanics-molecular mechanics (QM/MM) calculations. The results give hints to the physical forces of functional group distinctions and starting points for later parameter optimizations. The demonstrated technology significantly extends the manageability of accurate, but costly quantum chemical calculations and is valuable for many applications involving thousands of independent runs.</Para></Abstract></ChapterHeader><NoBody></NoBody></Chapter></Part></Book></Series></Publisher></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Applying Grid Computing to the Parameter Sweep of a Group Difference Pseudopotential</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>Applying Grid Computing to the Parameter Sweep of a Group Difference Pseudopotential</title></titleInfo><name type="personal"><namePart type="given">Wibke</namePart><namePart type="family">Sudholt</namePart><affiliation>Department of Chemistry & Biochemistry and San Diego Supercomputer Center (SDSC), University of California, San Diego (UCSD), 9500 Gilman Dr, 92093-0505, La Jolla, CA, USA</affiliation><affiliation>E-mail: wibke@sdsc.edu</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Kim</namePart><namePart type="given">K.</namePart><namePart type="family">Baldridge</namePart><affiliation>Department of Chemistry & Biochemistry and San Diego Supercomputer Center (SDSC), University of California, San Diego (UCSD), 9500 Gilman Dr, 92093-0505, La Jolla, CA, USA</affiliation><affiliation>E-mail: kimb@sdsc.edu</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">David</namePart><namePart type="family">Abramson</namePart><affiliation>Center for Enterprise Distributed Systems (DSTC) and School of Computer Science and Software Engineering, Monash University, 3800, Clayton, Victoria, Australia</affiliation><affiliation>E-mail: davida@csse.monash.edu.au</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Colin</namePart><namePart type="family">Enticott</namePart><affiliation>Center for Enterprise Distributed Systems (DSTC) and School of Computer Science and Software Engineering, Monash University, 3800, Clayton, Victoria, Australia</affiliation><affiliation>E-mail: Colin.Enticott@csse.monash.edu.au</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Slavisa</namePart><namePart type="family">Garic</namePart><affiliation>Center for Enterprise Distributed Systems (DSTC) and School of Computer Science and Software Engineering, Monash University, 3800, Clayton, Victoria, Australia</affiliation><affiliation>E-mail: Slavisa.Garic@infotech.monash.edu.au</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="conference" displayLabel="OriginalPaper"></genre><originInfo><publisher>Springer Berlin Heidelberg</publisher><place><placeTerm type="text">Berlin, Heidelberg</placeTerm></place><dateIssued encoding="w3cdtf">2004</dateIssued><copyrightDate encoding="w3cdtf">2004</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><physicalDescription><internetMediaType>text/html</internetMediaType></physicalDescription><abstract lang="en">Abstract: Theoretical modeling of chemical and biological processes is a key to understand nature and to predict experiments. Unfortunately, this is very data and computation extensive. However, the worldwide computing grid can now provide the necessary resources. Here, we present a coupling of the GAMESS quantum chemical code to the Nimrod/G grid distribution tool, which is applied to the parameter scan of a group difference pseudopotential (GDP). This represents the initial step in parameterization of a capping atom for hybrid quantum mechanics-molecular mechanics (QM/MM) calculations. The results give hints to the physical forces of functional group distinctions and starting points for later parameter optimizations. The demonstrated technology significantly extends the manageability of accurate, but costly quantum chemical calculations and is valuable for many applications involving thousands of independent runs.</abstract><relatedItem type="host"><titleInfo><title>Computational Science - ICCS 2004</title><subTitle>4th International Conference, Kraków, Poland, June 6-9, 2004, Proceedings, Part I</subTitle></titleInfo><name type="personal"><namePart type="given">Marian</namePart><namePart type="family">Bubak</namePart><affiliation>Institute of Computer Science, AGH, Poland</affiliation><affiliation>E-mail: bubak@science.uva.nl</affiliation><role><roleTerm type="text">editor</roleTerm></role></name><name type="personal"><namePart type="given">Geert</namePart><namePart type="given">Dick</namePart><namePart type="family">van Albada</namePart><affiliation>Department of Mathematics and Computer Science, University of Amsterdam, Kruislaan 403, 1098 SJ, Amsterdam, The 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