Promoting transparency and reproducibility in enhanced molecular simulations

Bonomi, Massimiliano; Bussi, Giovanni; Bernetti, Mattia; Cesari, Andrea; Laio, Alessandro; Camilloni, Carlo; Paissoni, Cristina; A. Tribello, Gareth; Banáš, Pavel; Barducci, Alessandro; G. Bolhuis, Peter; Ensing, Bernd; Bottaro, Sandro; H Parrinello, M; Branduardi, Davide; Capelli, Riccardo; Carloni, Paolo; Ceriotti, Michele; Giberti, Federico; Chen, Haochuan; Fu, Haohao; C Chen, W; Colizzi, Francesco; De, Sandip; De La Pierre, Marco; Donadio, Davide; Drobot, Viktor; L. Ferguson, Andrew; Filizola, Marta; Provasi, Davide; S. Fraser, James; Gasparotto, Piero; Michaelides, Angelos; Salvalaglio, Matteo; Luigi Gervasio, Francesco; Gil-Ley, Alejandro; Marinelli, Fabrizio; Giorgino, Toni; T. Heller, Gabriella; Löhr, Thomas; Vendruscolo, Michele; M. Hocky, Glen; Iannuzzi, Marcella; Invernizzi, Michele; Piaggi, Pablo; Piccini, GiovanniMaria; E. Jelfs, Kim; Jussupow, Alexander; Kirilin, Evgeny; Limongelli, Vittorio; Raniolo, Stefano; Lindorff‐Larsen, Kresten; Martin‐Samos, Layla; Masetti, Matteo; Meyer, Ralf; Molteni, Carla; Morishita, Tetsuya; Nava, Marco; Papaleo, Elena; Pfaendtner, Jim; Pietropaolo, Adriana; Pietrucci, Fabio; Pipolo, Silvio; Quigley, David; Raiteri, Paolo; Rydzewski, Jakub; C. Sosso, Gabriele; Spiwok, Vojtěch; Sponer, J; W. Swenson, David; Pk, Tiwary; Valsson, Ómar; A. Voth, Gregory; White, Andrew

doi:10.1038/s41592-019-0506-8

Public

Promoting transparency and reproducibility in enhanced molecular simulations

Published in Nature Methods • Jul 30, 2019

Authors:

Massimiliano Bonomi

Giovanni Bussi

Mattia Bernetti

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 enha...

Subject

Transparency (behavior)

Reproducibility

Molecular dynamics

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