Promoting transparency and reproducibility in enhanced molecular simulations

© 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 reproducibili...

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Main Authors:	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.
Format:	Journal Article
Language:	English
Published:	NATURE PUBLISHING GROUP 2019
Subjects:	Science & Technology Life Sciences & Biomedicine Biochemical Research Methods Biochemistry & Molecular Biology DYNAMICS
Online Access:	http://hdl.handle.net/20.500.11937/77070

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author	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.
author_facet	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.
author_sort	Bonomi, M.
building	Curtin Institutional Repository
collection	Online Access
description	© 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.
first_indexed	2025-11-14T11:09:25Z
format	Journal Article
id	curtin-20.500.11937-77070
institution	Curtin University Malaysia
institution_category	Local University
language	English
last_indexed	2025-11-14T11:09:25Z
publishDate	2019
publisher	NATURE PUBLISHING GROUP
recordtype	eprints
repository_type	Digital Repository
spelling	curtin-20.500.11937-770702020-01-31T05:40:06Z 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. Science & Technology Life Sciences & Biomedicine Biochemical Research Methods Biochemistry & Molecular Biology DYNAMICS © 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. 2019 Journal Article http://hdl.handle.net/20.500.11937/77070 10.1038/s41592-019-0506-8 English NATURE PUBLISHING GROUP fulltext
spellingShingle	Science & Technology Life Sciences & Biomedicine Biochemical Research Methods Biochemistry & Molecular Biology DYNAMICS 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. Promoting transparency and reproducibility in enhanced molecular simulations
title	Promoting transparency and reproducibility in enhanced molecular simulations
title_full	Promoting transparency and reproducibility in enhanced molecular simulations
title_fullStr	Promoting transparency and reproducibility in enhanced molecular simulations
title_full_unstemmed	Promoting transparency and reproducibility in enhanced molecular simulations
title_short	Promoting transparency and reproducibility in enhanced molecular simulations
title_sort	promoting transparency and reproducibility in enhanced molecular simulations
topic	Science & Technology Life Sciences & Biomedicine Biochemical Research Methods Biochemistry & Molecular Biology DYNAMICS
url	http://hdl.handle.net/20.500.11937/77070

Promoting transparency and reproducibility in enhanced molecular simulations

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