Promoting transparency and reproducibility in enhanced molecular simulations

Bonomi, M.; Bussi, G.; Camilloni, C.; Tribello, G.A.; Banáš, P.; Barducci, A.; Bernetti, M.; Bolhuis, P.G.; Bottaro, S.; Branduardi, D.; Capelli, R.; Carloni, P.; Ceriotti, M.; Cesari, A.; Chen, H.; Chen, W.; Colizzi, F.; De, S.; De La Pierre, M.; Donadio, D.; Drobot, V.; Ensing, B.; Ferguson, A.L.; Filizola, M.; Fraser, J.S.; Fu, H.; Gasparotto, P.; Gervasio, F.L.; Giberti, F.; Gil-Ley, A.; Giorgino, T.; Heller, G.T.; Hocky, G.M.; Iannuzzi, M.; Invernizzi, M.; Jelfs, K.E.; Jussupow, A.; Kirilin, E.; Laio, A.; Limongelli, V.; Lindorff-Larsen, K.; Löhr, T.; Marinelli, F.; Martin-Samos, L.; Masetti, M.; Meyer, R.; Michaelides, A.; Molteni, C.; Morishita, T.; Nava, M.; Paissoni, C.; Papaleo, E.; Parrinello, M.; Pfaendtner, J.; Piaggi, P.; Piccini, G.M.; Pietropaolo, A.; Pietrucci, F.; Pipolo, S.; Provasi, D.; Quigley, D.; Raiteri, Paolo; Raniolo, S.; Rydzewski, J.; Salvalaglio, M.; Sosso, G.C.; Spiwok, V.; Šponer, J.; Swenson, D.W.H.; Tiwary, P.; Valsson, O.; Vendruscolo, M.; Voth, G.A.; White, A.

doi:10.1038/s41592-019-0506-8

dc.contributor.author	Bonomi, M.
dc.contributor.author	Bussi, G.
dc.contributor.author	Camilloni, C.
dc.contributor.author	Tribello, G.A.
dc.contributor.author	Banáš, P.
dc.contributor.author	Barducci, A.
dc.contributor.author	Bernetti, M.
dc.contributor.author	Bolhuis, P.G.
dc.contributor.author	Bottaro, S.
dc.contributor.author	Branduardi, D.
dc.contributor.author	Capelli, R.
dc.contributor.author	Carloni, P.
dc.contributor.author	Ceriotti, M.
dc.contributor.author	Cesari, A.
dc.contributor.author	Chen, H.
dc.contributor.author	Chen, W.
dc.contributor.author	Colizzi, F.
dc.contributor.author	De, S.
dc.contributor.author	De La Pierre, M.
dc.contributor.author	Donadio, D.
dc.contributor.author	Drobot, V.
dc.contributor.author	Ensing, B.
dc.contributor.author	Ferguson, A.L.
dc.contributor.author	Filizola, M.
dc.contributor.author	Fraser, J.S.
dc.contributor.author	Fu, H.
dc.contributor.author	Gasparotto, P.
dc.contributor.author	Gervasio, F.L.
dc.contributor.author	Giberti, F.
dc.contributor.author	Gil-Ley, A.
dc.contributor.author	Giorgino, T.
dc.contributor.author	Heller, G.T.
dc.contributor.author	Hocky, G.M.
dc.contributor.author	Iannuzzi, M.
dc.contributor.author	Invernizzi, M.
dc.contributor.author	Jelfs, K.E.
dc.contributor.author	Jussupow, A.
dc.contributor.author	Kirilin, E.
dc.contributor.author	Laio, A.
dc.contributor.author	Limongelli, V.
dc.contributor.author	Lindorff-Larsen, K.
dc.contributor.author	Löhr, T.
dc.contributor.author	Marinelli, F.
dc.contributor.author	Martin-Samos, L.
dc.contributor.author	Masetti, M.
dc.contributor.author	Meyer, R.
dc.contributor.author	Michaelides, A.
dc.contributor.author	Molteni, C.
dc.contributor.author	Morishita, T.
dc.contributor.author	Nava, M.
dc.contributor.author	Paissoni, C.
dc.contributor.author	Papaleo, E.
dc.contributor.author	Parrinello, M.
dc.contributor.author	Pfaendtner, J.
dc.contributor.author	Piaggi, P.
dc.contributor.author	Piccini, G.M.
dc.contributor.author	Pietropaolo, A.
dc.contributor.author	Pietrucci, F.
dc.contributor.author	Pipolo, S.
dc.contributor.author	Provasi, D.
dc.contributor.author	Quigley, D.
dc.contributor.author	Raiteri, Paolo
dc.contributor.author	Raniolo, S.
dc.contributor.author	Rydzewski, J.
dc.contributor.author	Salvalaglio, M.
dc.contributor.author	Sosso, G.C.
dc.contributor.author	Spiwok, V.
dc.contributor.author	Šponer, J.
dc.contributor.author	Swenson, D.W.H.
dc.contributor.author	Tiwary, P.
dc.contributor.author	Valsson, O.
dc.contributor.author	Vendruscolo, M.
dc.contributor.author	Voth, G.A.
dc.contributor.author	White, A.
dc.date.accessioned	2019-12-02T05:04:14Z
dc.date.available	2019-12-02T05:04:14Z
dc.date.issued	2019
dc.identifier.citation	Bonomi, M. and Bussi, G. and Camilloni, C. and Tribello, G.A. and Banáš, P. and Barducci, A. and Bernetti, M. et al. 2019. Promoting transparency and reproducibility in enhanced molecular simulations. Nature Methods. 16 (8): pp. 670-673.
dc.identifier.uri	http://hdl.handle.net/20.500.11937/77070
dc.identifier.doi	10.1038/s41592-019-0506-8
dc.description.abstract	© 2019, Springer Nature America, Inc. The PLUMED consortium unifies developers and contributors to PLUMED, an open-source library for enhanced-sampling, free-energy calculations and the analysis of molecular dynamics simulations. Here, we outline our efforts to promote transparency and reproducibility by disseminating protocols for enhanced-sampling molecular simulations.
dc.language	English
dc.publisher	NATURE PUBLISHING GROUP
dc.subject	Science & Technology
dc.subject	Life Sciences & Biomedicine
dc.subject	Biochemical Research Methods
dc.subject	Biochemistry & Molecular Biology
dc.subject	DYNAMICS
dc.title	Promoting transparency and reproducibility in enhanced molecular simulations
dc.type	Journal Article
dcterms.source.volume	16
dcterms.source.number	8
dcterms.source.startPage	670
dcterms.source.endPage	673
dcterms.source.issn	1548-7091
dcterms.source.title	Nature Methods
dc.date.updated	2019-12-02T05:04:14Z
curtin.department	School of Molecular and Life Sciences (MLS)
curtin.accessStatus	Open access
curtin.faculty	Faculty of Science and Engineering
curtin.contributor.orcid	Raiteri, Paolo [0000-0003-0692-0505]
curtin.contributor.researcherid	Raiteri, Paolo [E-1465-2011]
dcterms.source.eissn	1548-7105
curtin.contributor.scopusauthorid	Raiteri, Paolo [6602613407]

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