Please use this identifier to cite or link to this item: http://repositorio.unicamp.br/jspui/handle/REPOSIP/1078
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dc.contributor.CRUESPUNIVERSIDADE ESTADUAL DE CAMPINASpt_BR
dc.subject.otherIONIC LIQUIDen
dc.subject.otherALGORITHMen
dc.subject.otherOPTIMIZATIONen
dc.subject.otherINTERFACEen
dc.subject.otherDOCKINGen
dc.subject.otherBINDINGen
dc.subject.otherMODELen
dc.typeArtigo de periódicopt_BR
dc.type.categoryoriginal articlept_BR
dc.type.versionpublishedVersionpt_BR
dc.titlePACKMOL: A Package for Building Initial Configurations for Molecular Dynamics Simulationspt_BR
dc.contributor.authorMARTINEZ, L.pt_BR
dc.contributor.authorANDRADE, R.pt_BR
dc.contributor.authorBIRGIN, E. G.pt_BR
dc.contributor.authorMARTINEZ, J. M.pt_BR
unicamp.authorMARTINEZ, L.:Universidade Estadual de Campinas, Instituto de Química, Departamento de Físico-Químicapt_BR
unicamp.authorMARTINEZ, J. M.:Universidade Estadual de Campinas, Instituto de Matemática, Estatística e Computação Científica, Departamento de Matemática Aplicadapt_BR
unicamp.author.externalANDRADE, R.pt
unicamp.author.externalBIRGIN, E. G.pt
dc.subjectinitial configurationpt_BR
dc.subjectmolecular dynamicspt_BR
dc.subjectpackingpt_BR
dc.subjectlarge-scale optimizationpt_BR
dc.subjectPACKMOLpt_BR
dc.subject.wosChemistry, Multidisciplinarypt_BR
dc.description.abstractAdequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system`s overall structure. In order that the simulations are not disrupted by large van der Waals repulsive interactions, atoms from different molecules Must keep safe pairwise distances. Obtaining Such a molecular arrangement can be considered it packing problem: Each type molecule must satisfy spatial constraints related to the geometry of the system, and the distance between atoms of different molecules Must be greater than some specified tolerance. We have developed a code able to pack millions of atoms. grouped in arbitrarily complex molecules, inside a variety of three-dimensional regions. The regions may be intersections of spheres, ellipses, cylinders, planes, or boxes. The user must provide only the structure of one molecule of each type and the geometrical constraints that each type of molecule must satisfy. Building complex mixtures, interfaces, solvating biomolecules in water, other solvents, or mixtures of solvents, is straight forward. In addition. different atoms belonging to the same molecule may also be restricted to different spatial regions, in Such a way that more ordered molecular arrangements call be built, as micelles. lipid double-layers, etc. The packing time for state-of-the-art molecular dynamics systems varies front a few seconds to a few Minutes in a personal Computer. The input files are simple and Currently compatible with PDB, Tinker, Molden, or Moldy coordinate files. The package is distributed as free software and call be downloaded front http://www.ime.unicamp.br/similar to martinez/packmol/. (C) 2009 Wiley Periodicals. Inc. J Comput Chem 30: 2157-2164, 2009en
dc.relation.ispartofJournal of Computational Chemistrypt_BR
dc.publisher.countryEstados Unidospt_BR
dc.publisherJOHN WILEY & SONS INCpt_BR
dc.date.issued2009pt_BR
dc.identifier.citationJOURNAL OF COMPUTATIONAL CHEMISTRY, v.30, n.13, p.2157-2164, 2009pt_BR
dc.language.isoengpt_BR
dc.description.volume30pt_BR
dc.description.issuenumber13pt_BR
dc.description.firstpage2157pt_BR
dc.description.lastpage2164pt_BR
dc.rightsfechadopt_BR
dc.rights.holderCopyright JOHN WILEY & SONS INCpt_BR
dc.sourceWOSpt_BR
unicamp.cruespUSPpt_BR
dc.identifier.issn0192-8651pt_BR
dc.identifier.doi10.1002/jcc.21224pt_BR
dc.identifier.urlhttp://dx.doi.org/10.1002/jcc.21224pt_BR
dc.identifier.urlhttp://apps.isiknowledge.com/InboundService.do?Func=Frame&product=WOS&action=retrieve&SrcApp=EndNote&UT=000269095700020&Init=Yes&SrcAuth=ResearchSoft&mode=FullRecordpt_BR
dc.description.sponsorshipCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)pt_BR
dc.description.sponsorshipConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)pt_BR
dc.description.sponsorshipFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)pt_BR
dc.description.sponsorship1Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)pt_BR
dc.description.sponsorship1Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)pt_BR
dc.description.sponsorship1Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)pt_BR
dc.date.available2013-07-26T17:59:38Z
dc.date.available2016-07-01T12:53:30Z-
dc.date.accessioned2013-07-26T17:59:38Z
dc.date.accessioned2016-07-01T12:53:30Z-
dc.description.provenanceMade available in DSpace on 2013-07-26T17:59:38Z (GMT). No. of bitstreams: 2 art_MARTINEZ_PACKMOL_A_Package_for_Building_Initial_Configurations_2009.pdf.txt: 36431 bytes, checksum: 9ce37afd44b46e0623452bff74dd145b (MD5) art_MARTINEZ_PACKMOL_A_Package_for_Building_Initial_Configurations_2009.pdf: 236838 bytes, checksum: 86c01452352e1e6d8c24ff6044136b80 (MD5) Previous issue date: 2009en
dc.description.provenanceMade available in DSpace on 2016-07-01T12:53:30Z (GMT). No. of bitstreams: 2 art_MARTINEZ_PACKMOL_A_Package_for_Building_Initial_Configurations_2009.pdf.txt: 36431 bytes, checksum: 9ce37afd44b46e0623452bff74dd145b (MD5) art_MARTINEZ_PACKMOL_A_Package_for_Building_Initial_Configurations_2009.pdf: 236838 bytes, checksum: 86c01452352e1e6d8c24ff6044136b80 (MD5) Previous issue date: 2009en
dc.identifier.urihttp://www.repositorio.unicamp.br/jspui/handle/REPOSIP/1078
dc.identifier.urihttp://repositorio.unicamp.br/jspui/handle/REPOSIP/1078-
dc.contributor.departmentFísico-Química
dc.contributor.unidadeIQpt
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