Please use this identifier to cite or link to this item: http://repositorio.unicamp.br/jspui/handle/REPOSIP/348515
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dc.contributor.CRUESPUNIVERSIDADE ESTADUAL DE CAMPINASpt_BR
dc.contributor.authorunicampMartínez, Leandro-
dc.contributor.authorunicampMartínez Pérez, José Mario-
dc.typeArtigopt_BR
dc.titlePACKMOL: a package for building initial configurations for molecular dynamics simulationspt_BR
dc.contributor.authorMartínez, L.-
dc.contributor.authorAndrade, R.-
dc.contributor.authorBirgin, E. G.-
dc.contributor.authorMartínez, J. M.-
dc.subjectDinâmica molecularpt_BR
dc.subject.otherlanguageMolecular dynamicspt_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 a 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 straightforward. 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 can be built, as micelles, lipid double‐layers, etc. The packing time for state‐of‐the‐art molecular dynamics systems varies from 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 can be downloaded from http://www.ime.unicamp.br/∼martinez/packmol/pt_BR
dc.relation.ispartofJournal of computational chemistrypt_BR
dc.relation.ispartofabbreviationJ. comput. chem.pt_BR
dc.publisher.cityNew York, NYpt_BR
dc.publisher.countryEstados Unidospt_BR
dc.publisherJohn Wiley & Sonspt_BR
dc.date.issued2009-
dc.date.monthofcirculationOct.pt_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.sourceWOSpt_BR
dc.identifier.issn0192-8651pt_BR
dc.identifier.eissn1096-987Xpt_BR
dc.identifier.doi10.1002/jcc.21224pt_BR
dc.identifier.urlhttps://onlinelibrary.wiley.com/doi/full/10.1002/jcc.21224pt_BR
dc.description.sponsorshipCONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQpt_BR
dc.description.sponsorshipCOORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIOR - CAPESpt_BR
dc.description.sponsorshipFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESPpt_BR
dc.description.sponsordocumentnumberSem informaçãopt_BR
dc.description.sponsordocumentnumberSem informaçãopt_BR
dc.description.sponsordocumentnumberSem informaçãopt_BR
dc.date.available2020-09-02T12:46:37Z-
dc.date.accessioned2020-09-02T12:46:37Z-
dc.description.provenanceSubmitted by Thais de Brito Barroso (tbrito@unicamp.br) on 2020-09-02T12:46:37Z No. of bitstreams: 0. Added 1 bitstream(s) on 2021-01-04T15:12:16Z : No. of bitstreams: 1 000269095700020.pdf: 314713 bytes, checksum: 0a6369e3bd331e2f1ae6a783b2707630 (MD5)en
dc.description.provenanceMade available in DSpace on 2020-09-02T12:46:37Z (GMT). No. of bitstreams: 0 Previous issue date: 2009en
dc.identifier.urihttp://repositorio.unicamp.br/jspui/handle/REPOSIP/348515-
dc.contributor.departmentDepartamento de Físico-Químicapt_BR
dc.contributor.departmentDepartamento de Matemática Aplicadapt_BR
dc.contributor.unidadeInstituto de Químicapt_BR
dc.contributor.unidadeInstituto de Matemática, Estatística e Computação Científicapt_BR
dc.subject.keywordInitial configurationpt_BR
dc.subject.keywordPackingpt_BR
dc.subject.keywordLarge-scale optimizationpt_BR
dc.subject.keywordPACKMOLpt_BR
dc.identifier.source000269095700020pt_BR
dc.creator.orcid0000-0002-6857-1884pt_BR
dc.creator.orcid0000-0003-3331-368Xpt_BR
dc.type.formArtigopt_BR
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