Peer-Reviewed Publication
J Chem Phys2025;162(9)March 7, 2025Journal Article
PLUMED Tutorials: A collaborative, community-driven learning ecosystem.
Gareth A Tribello1, Massimiliano Bonomi2, Giovanni Bussi3, Carlo Camilloni4, Blake I Armstrong5, Andrea Arsiccio6, Simone Aureli7,8,9, Federico Ballabio1,4,10, Mattia Bernetti1, Luigi Bonati11, Samuel G H Brookes1, Z Faidon Brotzakis1, Riccardo Capelli4, Michele Ceriotti12, Kam-Tung Chan13, Pilar Cossio1,2, Siva Dasetty14, Davide Donadio13, Bernd Ensing2, Andrew L Ferguson2, Guillaume Fraux1,2, Julian D Gale5, Francesco Luigi Gervasio2,7,8,9, Toni Giorgino10, Nicholas S M Herringer15, Glen M Hocky16, Samuel E Hoff2, Michele Invernizzi17, Olivier Languin-Cattoën3, Vanessa Leone18, Vittorio Limongelli19, Olga Lopez-Acevedo20, Fabrizio Marinelli18, Pedro Febrer Martinez7,8,9, Matteo Masetti21, Shams Mehdi22, Angelos Michaelides23, Mhd Hussein Murtada24, Michele Parrinello11, Pablo M Piaggi25, Adriana Pietropaolo26, Fabio Pietrucci27, Silvio Pipolo28, Claire Pritchard29, Paolo Raiteri5, Stefano Raniolo19, Daniele Rapetti3, Valerio Rizzi7,8,9, Jakub Rydzewski30, Matteo Salvalaglio31, Christoph Schran32, Aniruddha Seal15, Armin Shayesteh Zadeh14, Tomás F D Silva3, Vojtěch Spiwok33, Guillaume Stirnemann29, Daniel Sucerquia34, Pratyush Tiwary22, Omar Valsson35, Michele Vendruscolo24, Gregory A Voth36, Andrew D White37, Jiangbo Wu36
1Centre for Quantum Materials and Technologies, School of Mathematics and Physics, Queen's University Belfast, Belfast, United Kingdom.
2Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Computational Structural Biology Unit, Paris, France.
3Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy.
4Department of Biosciences, University of Milano, Milano, Italy.
5School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia.
6Coriolis Pharma, Fraunhoferstrasse 18b, 82152 Martinsried, Germany.
7School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, CH-1206 Geneva, Switzerland.
8Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CH-1206 Geneva, Switzerland.
9Swiss Bioinformatics Institute, University of Geneva, CH-1206 Geneva, Switzerland.
10National Research Council of Italy, Biophysics Institute (CNR-IBF), Via Celoria 26, Milan 20133, Italy.
11Atomistic Simulations, Italian Institute of Technology, Genova, Italy.
12Laboratory of Computational Science and Modeling, Institut des Matériaux, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
13Department of Chemistry, University of California, Davis, Davis, California 95616, USA.
14Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA.
15Department of Chemistry, University of Chicago, Chicago, Illinois 60637, USA.
16Department of Chemistry, Simons Center for Computational Physical Chemistry, New York University, New York, New York 10012, USA.
17Peptone Ltd., The Connolly Works 41-43, Chalton Street, London NW1 1JD, United Kingdom.
18Department of Biophysics and Data Science Institute, Medical College of Wisconsin, Milwaukee, Wisconsin 53226-3548, USA.
19Euler Institute, Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), via G. Buffi 13, CH-6900 Lugano, Switzerland.
20Biophysics of Tropical Diseases Max Planck Tandem Group, University of Antioquia UdeA, 050010 Medellin, Colombia.
21Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy.
22Department of Chemistry and Biochemistry, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA.
23Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom.
24Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.
25CIC nanoGUNE BRTA, Tolosa Hiribidea 76, 20018 Donostia-San Sebastián, Spain and Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain.
26Dipartimento di Scienze della Salute, Università Magna Graecia di Catanzaro, Viale Europa, 88100 Catanzaro, Italy.
27Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris 75005, France.
28UCCS Unité de Catalyse et Chimie du Solide, Université de Lille, Université d'Artois UMR 8181, F-59000 Lille, France.
29PASTEUR, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24 rue Lhomond, 75005 Paris, France.
30Faculty of Physics, Astronomy and Informatics, Institute of Physics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Toruń, Poland.
31Thomas Young Centre and Department of Chemical Engineering, University College London, London WC1E 7JE, United Kingdom.
32Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom.
33University of Chemistry and Technology, Technická 5, CZ-166 28 Praha 6, Czech Republic.
34Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany.
35Department of Chemistry, University of North Texas, Denton, Texas 76201, USA.
36Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, University of Chicago, Chicago, Illinois 60637, USA.
37Department of Chemical Engineering, University of Rochester, Rochester, New York 14627, USA.
Abstract
In computational physics, chemistry, and biology, the implementation of new techniques in shared and open-source software lowers barriers to entry and promotes rapid scientific progress. However, effectively training new software users presents several challenges. Common methods like direct knowledge transfer and in-person workshops are limited in reach and comprehensiveness. Furthermore, while th…
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