PLUMED Tutorials: A collaborative, community-driven learning ecosystem

Gareth A Tribello¹, Massimiliano Bonomi², Giovanni Bussi³, Carlo Camilloni⁴, Blake I Armstrong⁵, Andrea Arsiccio⁶, Simone Aureli^{7

8

9}, Federico Ballabio^{1

4

10}, Mattia Bernetti¹, Luigi Bonati¹¹, Samuel G H Brookes¹, Z Faidon Brotzakis¹, Riccardo Capelli⁴, Michele Ceriotti¹², Kam-Tung Chan¹³, Pilar Cossio^{1

2}, Siva Dasetty¹⁴, Davide Donadio¹³, Bernd Ensing², Andrew L Ferguson², Guillaume Fraux^{1

2}, Julian D Gale⁵, Francesco Luigi Gervasio^{2

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 Martinez^{7

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 Rizzi^{7

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

Affiliations

¹ Centre for Quantum Materials and Technologies, School of Mathematics and Physics, Queen's University Belfast, Belfast, United Kingdom.
² Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Computational Structural Biology Unit, Paris, France.
³ Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy.
⁴ Department of Biosciences, University of Milano, Milano, Italy.
⁵ School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia.
⁶ Coriolis Pharma, Fraunhoferstrasse 18b, 82152 Martinsried, Germany.
⁷ School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, CH-1206 Geneva, Switzerland.
⁸ Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CH-1206 Geneva, Switzerland.
⁹ Swiss Bioinformatics Institute, University of Geneva, CH-1206 Geneva, Switzerland.
¹⁰ National Research Council of Italy, Biophysics Institute (CNR-IBF), Via Celoria 26, Milan 20133, Italy.
¹¹ Atomistic Simulations, Italian Institute of Technology, Genova, Italy.
¹² Laboratory of Computational Science and Modeling, Institut des Matériaux, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
¹³ Department of Chemistry, University of California, Davis, Davis, California 95616, USA.
¹⁴ Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA.
¹⁵ Department of Chemistry, University of Chicago, Chicago, Illinois 60637, USA.
¹⁶ Department of Chemistry, Simons Center for Computational Physical Chemistry, New York University, New York, New York 10012, USA.
¹⁷ Peptone Ltd., The Connolly Works 41-43, Chalton Street, London NW1 1JD, United Kingdom.
¹⁸ Department of Biophysics and Data Science Institute, Medical College of Wisconsin, Milwaukee, Wisconsin 53226-3548, USA.
¹⁹ Euler Institute, Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), via G. Buffi 13, CH-6900 Lugano, Switzerland.
²⁰ Biophysics of Tropical Diseases Max Planck Tandem Group, University of Antioquia UdeA, 050010 Medellin, Colombia.
²¹ Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy.
²² Department of Chemistry and Biochemistry, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA.
²³ Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom.
²⁴ Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.
²⁵ CIC nanoGUNE BRTA, Tolosa Hiribidea 76, 20018 Donostia-San Sebastián, Spain and Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain.
²⁶ Dipartimento di Scienze della Salute, Università Magna Graecia di Catanzaro, Viale Europa, 88100 Catanzaro, Italy.
²⁷ Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris 75005, France.
²⁸ UCCS Unité de Catalyse et Chimie du Solide, Université de Lille, Université d'Artois UMR 8181, F-59000 Lille, France.
²⁹ PASTEUR, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24 rue Lhomond, 75005 Paris, France.
³⁰ Faculty of Physics, Astronomy and Informatics, Institute of Physics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Toruń, Poland.
³¹ Thomas Young Centre and Department of Chemical Engineering, University College London, London WC1E 7JE, United Kingdom.
³² Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom.
³³ University of Chemistry and Technology, Technická 5, CZ-166 28 Praha 6, Czech Republic.
³⁴ Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany.
³⁵ Department of Chemistry, University of North Texas, Denton, Texas 76201, USA.
³⁶ Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, University of Chicago, Chicago, Illinois 60637, USA.
³⁷ Department of Chemical Engineering, University of Rochester, Rochester, New York 14627, USA.

PMID: 40035582
PMCID: PMC12317779 (available on 2026-03-07)
DOI: 10.1063/5.0251501

PLUMED Tutorials: A collaborative, community-driven learning ecosystem

Gareth A Tribello et al. J Chem Phys. 2025.

. 2025 Mar 7;162(9):092501.

doi: 10.1063/5.0251501.

Authors

Affiliations

¹ Centre for Quantum Materials and Technologies, School of Mathematics and Physics, Queen's University Belfast, Belfast, United Kingdom.
² Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Computational Structural Biology Unit, Paris, France.
³ Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy.
⁴ Department of Biosciences, University of Milano, Milano, Italy.
⁵ School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia.
⁶ Coriolis Pharma, Fraunhoferstrasse 18b, 82152 Martinsried, Germany.
⁷ School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, CH-1206 Geneva, Switzerland.
⁸ Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CH-1206 Geneva, Switzerland.
⁹ Swiss Bioinformatics Institute, University of Geneva, CH-1206 Geneva, Switzerland.
¹⁰ National Research Council of Italy, Biophysics Institute (CNR-IBF), Via Celoria 26, Milan 20133, Italy.
¹¹ Atomistic Simulations, Italian Institute of Technology, Genova, Italy.
¹² Laboratory of Computational Science and Modeling, Institut des Matériaux, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
¹³ Department of Chemistry, University of California, Davis, Davis, California 95616, USA.
¹⁴ Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA.
¹⁵ Department of Chemistry, University of Chicago, Chicago, Illinois 60637, USA.
¹⁶ Department of Chemistry, Simons Center for Computational Physical Chemistry, New York University, New York, New York 10012, USA.
¹⁷ Peptone Ltd., The Connolly Works 41-43, Chalton Street, London NW1 1JD, United Kingdom.
¹⁸ Department of Biophysics and Data Science Institute, Medical College of Wisconsin, Milwaukee, Wisconsin 53226-3548, USA.
¹⁹ Euler Institute, Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), via G. Buffi 13, CH-6900 Lugano, Switzerland.
²⁰ Biophysics of Tropical Diseases Max Planck Tandem Group, University of Antioquia UdeA, 050010 Medellin, Colombia.
²¹ Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy.
²² Department of Chemistry and Biochemistry, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA.
²³ Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom.
²⁴ Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.
²⁵ CIC nanoGUNE BRTA, Tolosa Hiribidea 76, 20018 Donostia-San Sebastián, Spain and Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain.
²⁶ Dipartimento di Scienze della Salute, Università Magna Graecia di Catanzaro, Viale Europa, 88100 Catanzaro, Italy.
²⁷ Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris 75005, France.
²⁸ UCCS Unité de Catalyse et Chimie du Solide, Université de Lille, Université d'Artois UMR 8181, F-59000 Lille, France.
²⁹ PASTEUR, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24 rue Lhomond, 75005 Paris, France.
³⁰ Faculty of Physics, Astronomy and Informatics, Institute of Physics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Toruń, Poland.
³¹ Thomas Young Centre and Department of Chemical Engineering, University College London, London WC1E 7JE, United Kingdom.
³² Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom.
³³ University of Chemistry and Technology, Technická 5, CZ-166 28 Praha 6, Czech Republic.
³⁴ Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany.
³⁵ Department of Chemistry, University of North Texas, Denton, Texas 76201, USA.
³⁶ Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, University of Chicago, Chicago, Illinois 60637, USA.
³⁷ Department of Chemical Engineering, University of Rochester, Rochester, New York 14627, USA.

PMID: 40035582
PMCID: PMC12317779 (available on 2026-03-07)
DOI: 10.1063/5.0251501

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 the COVID-19 pandemic highlighted the benefits of online training, traditional online tutorials can quickly become outdated and may not cover all the software's functionalities. To address these issues, here we introduce "PLUMED Tutorials," a collaborative model for developing, sharing, and updating online tutorials. This initiative utilizes repository management and continuous integration to ensure compatibility with software updates. Moreover, the tutorials are interconnected to form a structured learning path and are enriched with automatic annotations to provide broader context. This paper illustrates the development, features, and advantages of PLUMED Tutorials, aiming to foster an open community for creating and sharing educational resources.

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Conflict of interest statement

A.L.F. is a co-founder and consultant of Evozyne, Inc. and a co-author of U.S. Patent Applications 16/887710 and 17/642582, U.S. Provisional Patent Applications 62/853919, 62/900420, 63/314898, 63/479378, 63/521617, and 63/669836, and International Patent Applications PCT/US2020/035206, PCT/US2020/050466, and PCT/US24/10805.

References

1. Bonomi M., Branduardi D., Bussi G., Camilloni C., Provasi D., Raiteri P., Donadio D., Marinelli F., Pietrucci F., Broglia R. A., and Parrinello M., “PLUMED: A portable plugin for free-energy calculations with molecular dynamics,” Comput. Phys. Commun. 180, 1961–1972 (2009). 10.1016/j.cpc.2009.05.011 - DOI
1. Tribello G. A., Bonomi M., Branduardi D., Camilloni C., and Bussi G., “PLUMED 2: New feathers for an old bird,” Comput. Phys. Commun. 185, 604–613 (2014). 10.1016/j.cpc.2013.09.018 - DOI
1. Schwarz M., Scherrer A., Hohmann C., Heiberg J., Brugger A., and Nuñez-Jimenez A., “COVID-19 and the academy: It is time for going digital,” Energy Res. Social Sci. 68, 101684 (2020). 10.1016/j.erss.2020.101684 - DOI - PMC - PubMed
1. Bussi G. and Branduardi D., Reviews in Computational Chemistry (John Wiley and Sons Ltd., 2015), Vol. 28, Chap. 1, pp. 1–49.
1. Barducci A., Pfaendtner J., and Bonomi M., in Molecular Modeling of Proteins, edited by Kukol A. (Springer, New York, NY, 2015), pp. 151–171.

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PLUMED Tutorials: A collaborative, community-driven learning ecosystem

Affiliations

PLUMED Tutorials: A collaborative, community-driven learning ecosystem

Authors

Affiliations

Abstract

Conflict of interest statement

References

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources