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dc.contributor.authorWinger, Moritz
dc.contributor.authorTrzesniak, Daniel
dc.contributor.authorBaron, Riccardo
dc.contributor.authorF. van Gunsteren, Wilfred
dc.date.accessioned2017-05-03T16:02:50Z
dc.date.available2017-05-03T16:02:50Z
dc.date.issued2009
dc.date.modified2012-07-27T03:06:00Z
dc.identifier.issn14639076
dc.identifier.doi10.1039/B818713D
dc.identifier.urihttp://hdl.handle.net/10072/37892
dc.description.abstractThe use of a coarse-grained (CG) model that is widely used in molecular dynamics simulations of biomolecular systems is investigated with respect to the dependence of a variety of quantities upon the size of the used integration time step and cutoff radius. The results suggest that when using a non-bonded interaction-cutoff radius of 1.4 nm a time step of maximally 10 fs should be used, in order not to produce energy sinks or wells. Using a too-large time step, e.g. 50 fs with a cutoff of 1.2 nm, as is done in the coarse-grained model of Marrink et al. (J. Phys. Chem. B, 2004, 108, 250 and 2007, 111, 7812), induces errors due to the linear approximation of the integrators that are commonly used to integrate the equations of motion. As a spin-off of the investigation of the mentioned CG models, we found that the parameters of the CG water model place it at physiological temperatures well into the solid phase of the phase diagram.
dc.description.peerreviewedYes
dc.description.publicationstatusYes
dc.format.extent681286 bytes
dc.format.mimetypeapplication/pdf
dc.languageEnglish
dc.language.isoeng
dc.publisherRoyal Society of Chemistry
dc.publisher.placeUnited Kingdom
dc.relation.ispartofstudentpublicationN
dc.relation.ispartofpagefrom1934
dc.relation.ispartofpageto1941
dc.relation.ispartofissue12
dc.relation.ispartofjournalPhysical Chemistry Chemical Physics
dc.relation.ispartofvolume11
dc.rights.retentionY
dc.subject.fieldofresearchBioinformatics Software
dc.subject.fieldofresearchPhysical Sciences
dc.subject.fieldofresearchChemical Sciences
dc.subject.fieldofresearchEngineering
dc.subject.fieldofresearchcode080301
dc.subject.fieldofresearchcode02
dc.subject.fieldofresearchcode03
dc.subject.fieldofresearchcode09
dc.titleOn using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models
dc.typeJournal article
dc.type.descriptionC1 - Articles
dc.type.codeC - Journal Articles
gro.rights.copyright© 2009 Royal Society of Chemistry. This is the author-manuscript version of this paper. Reproduced in accordance with the copyright policy of the publisher. Please refer to the journal website for access to the definitive, published version.
gro.date.issued2009
gro.hasfulltextFull Text
gro.griffith.authorWinger, Moritz


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