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Promoting transparency and reproducibility in enhanced molecular simulations
- Bonomi, Massimiliano;
- Bussi, Giovanni;
- Camilloni, Carlo;
- Tribello, Gareth A;
- Banas, Pavel;
- Barducci, Alessandro;
- Bernetti, Mattia;
- Bolhuis, Peter G;
- Bottaro, Sandro;
- Branduardi, Davide;
- Capelli, Riccardo;
- Carloni, Paolo;
- Ceriotti, Michele;
- Cesari, Andrea;
- Chen, Haochuan;
- Chen, Wei;
- Colizzi, Francesco;
- De, Sandip;
- De La Pierre, Marco;
- Donadio, Davide;
- Drobot, Viktor;
- Ensing, Bernd;
- Ferguson, Andrew L;
- Filizola, Marta;
- Fraser, James S;
- Fu, Haohao;
- Gasparotto, Piero;
- Gervasio, Francesco Luigi;
- Giberti, Federico;
- Gil-Ley, Alejandro;
- Giorgino, Toni;
- Heller, Gabriella T;
- Hocky, Glen M;
- Iannuzzi, Marcella;
- Invernizzi, Michele;
- Jelfs, Kim E;
- Jussupow, Alexander;
- Kirilin, Evgeny;
- Laio, Alessandro;
- Limongelli, Vittorio;
- Lindorff-Larsen, Kresten;
- Lohr, Thomas;
- Marinelli, Fabrizio;
- Martin-Samos, Layla;
- Masetti, Matteo;
- Meyer, Ralf;
- Michaelides, Angelos;
- Molteni, Carla;
- Morishita, Tetsuya;
- Nava, Marco;
- Paissoni, Cristina;
- Papaleo, Elena;
- Parrinello, Michele;
- Pfaendtner, Jim;
- Piaggi, Pablo;
- Piccini, GiovanniMaria;
- Pietropaolo, Adriana;
- Pietrucci, Fabio;
- Pipolo, Silvio;
- Provasi, Davide;
- Quigley, David;
- Raiteri, Paolo;
- Raniolo, Stefano;
- Rydzewski, Jakub;
- Salvalaglio, Matteo;
- Sosso, Gabriele Cesare;
- Spiwok, Vojtech;
- Sponer, Jiri;
- Swenson, David WH;
- Tiwary, Pratyush;
- Valsson, Omar;
- Vendruscolo, Michele;
- Voth, Gregory A;
- White, Andrew
- et al.
Published Web Location
https://doi.org/10.1038/s41592-019-0506-8Abstract
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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