Promoting transparency and reproducibility in enhanced molecular simulations

The PLUMED Consortium

doi:10.1038/s41592-019-0506-8

Promoting transparency and reproducibility in enhanced molecular simulations

The PLUMED Consortium

Institute of Experimental Physics (5110)

Research output: Contribution to journal › Comment/debate › peer-review

Abstract

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.

Original language	English
Pages (from-to)	670-673
Number of pages	4
Journal	Nature Methods
Volume	16
Issue number	8
DOIs	https://doi.org/10.1038/s41592-019-0506-8
Publication status	Published - 1 Aug 2019

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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10.1038/s41592-019-0506-8

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title = "Promoting transparency and reproducibility in enhanced molecular simulations",

abstract = "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.",

author = "{The PLUMED Consortium} and Massimiliano Bonomi and Giovanni Bussi and Carlo Camilloni and Tribello, {Gareth A.} and Pavel Ban{\'a}{\v s} and Alessandro Barducci and Mattia Bernetti and Bolhuis, {Peter G.} and Sandro Bottaro and Davide Branduardi and Riccardo Capelli and Paolo Carloni and Michele Ceriotti and Andrea Cesari and Haochuan Chen and Wei Chen and Francesco Colizzi and Sandip De and {De La Pierre}, Marco and Davide Donadio and Viktor Drobot and Bernd Ensing and Ferguson, {Andrew L.} and Marta Filizola and Fraser, {James S.} and Haohao Fu and Piero Gasparotto and Gervasio, {Francesco Luigi} and Federico Giberti and Alejandro Gil-Ley and Toni Giorgino and Heller, {Gabriella T.} and Hocky, {Glen M.} and Marcella Iannuzzi and Michele Invernizzi and Jelfs, {Kim E.} and Alexander Jussupow and Evgeny Kirilin and Alessandro Laio and Vittorio Limongelli and Kresten Lindorff-Larsen and Thomas L{\"o}hr and Fabrizio Marinelli and Layla Martin-Samos and Matteo Masetti and Ralf Meyer and Angelos Michaelides and Carla Molteni and Tetsuya Morishita and Marco Nava",

year = "2019",

month = aug,

day = "1",

doi = "10.1038/s41592-019-0506-8",

language = "English",

volume = "16",

pages = "670--673",

journal = "Nature Methods",

issn = "1548-7091",

publisher = "Nature Publishing Group",

number = "8",

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TY - JOUR

T1 - Promoting transparency and reproducibility in enhanced molecular simulations

AU - The PLUMED Consortium

AU - Bonomi, Massimiliano

AU - Bussi, Giovanni

AU - Camilloni, Carlo

AU - Tribello, Gareth A.

AU - Banáš, Pavel

AU - Barducci, Alessandro

AU - Bernetti, Mattia

AU - Bolhuis, Peter G.

AU - Bottaro, Sandro

AU - Branduardi, Davide

AU - Capelli, Riccardo

AU - Carloni, Paolo

AU - Ceriotti, Michele

AU - Cesari, Andrea

AU - Chen, Haochuan

AU - Chen, Wei

AU - Colizzi, Francesco

AU - De, Sandip

AU - De La Pierre, Marco

AU - Donadio, Davide

AU - Drobot, Viktor

AU - Ensing, Bernd

AU - Ferguson, Andrew L.

AU - Filizola, Marta

AU - Fraser, James S.

AU - Fu, Haohao

AU - Gasparotto, Piero

AU - Gervasio, Francesco Luigi

AU - Giberti, Federico

AU - Gil-Ley, Alejandro

AU - Giorgino, Toni

AU - Heller, Gabriella T.

AU - Hocky, Glen M.

AU - Iannuzzi, Marcella

AU - Invernizzi, Michele

AU - Jelfs, Kim E.

AU - Jussupow, Alexander

AU - Kirilin, Evgeny

AU - Laio, Alessandro

AU - Limongelli, Vittorio

AU - Lindorff-Larsen, Kresten

AU - Löhr, Thomas

AU - Marinelli, Fabrizio

AU - Martin-Samos, Layla

AU - Masetti, Matteo

AU - Meyer, Ralf

AU - Michaelides, Angelos

AU - Molteni, Carla

AU - Morishita, Tetsuya

AU - Nava, Marco

PY - 2019/8/1

Y1 - 2019/8/1

N2 - 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.

AB - 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.

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U2 - 10.1038/s41592-019-0506-8

DO - 10.1038/s41592-019-0506-8

M3 - Comment/debate

C2 - 31363226

AN - SCOPUS:85069961147

SN - 1548-7091

VL - 16

SP - 670

EP - 673

JO - Nature Methods

JF - Nature Methods

IS - 8

ER -

Promoting transparency and reproducibility in enhanced molecular simulations

Abstract

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