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Promoting transparency and reproducibility in enhanced molecular simulations

Nature Methods volume 16, pages 670–673 (2019)Cite this article

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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.

Molecular dynamics (MD) simulations have become an important tool for characterizing the mechanisms underlying complex processes, interpreting experimental measurements and predicting the behavior of molecular systems. This success has been achieved through more than 60 years of innovation. During this time, a wide community of researchers has developed accurate integrators of the equations of motion; effective thermostats; accurate physicochemical models of small molecules, proteins, nucleic acids, liquids and materials; many techniques to accelerate sampling; sophisticated analysis tools; powerful, personal and dedicated computers; and efficient, user-friendly software. These advances ensure that MD provides a powerful and versatile computational microscope that can be applied in fields ranging from physics and chemistry to biology and materials science.

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References

  1. Camilloni, C. & Pietrucci, F. Adv. Phys. X 3, 1477531 (2018).

    Google Scholar 

  2. Mittal, S. & Shukla, D. Mol. Simul. 44, 891–904 (2018).

    Article  CAS  Google Scholar 

  3. Bottaro, S. & Lindorff-Larsen, K. Science 361, 355–360 (2018).

    Article  CAS  Google Scholar 

  4. Grossfield, A. et al. Living J. Comput. Mol. Sci. 1, 5067 (2018).

    PubMed  PubMed Central  Google Scholar 

  5. Recommended data repositories. Scientific Data https://www.nature.com/sdata/policies/repositories (2019).

  6. Ollila, S. et al. Presentation slides from the workshop on “Sharing Data from Molecular Simulations”, Stockholm, 2018-11-27. Zenodo https://zenodo.org/record/2652703 (2018).

  7. Bonomi, M. et al. Comput. Phys. Commun. 180, 1961–1972 (2009).

    Article  CAS  Google Scholar 

  8. Fiorin, G., Klein, M. L. & Hénin, J. Mol. Phys. 111, 3345–3362 (2013).

    Article  CAS  Google Scholar 

  9. Sidky, H. et al. J. Chem. Phys. 148, 044104 (2018).

    Article  Google Scholar 

  10. Tribello, G. A., Bonomi, M., Branduardi, D., Camilloni, C. & Bussi, G. Comput. Phys. Commun. 185, 604–613 (2014).

    Article  CAS  Google Scholar 

  11. Harvey, M. J., Giupponi, G. & Fabritiis, G. D. J. Chem. Theory Comput. 5, 1632–1639 (2009).

    Article  CAS  Google Scholar 

  12. Case, D. A. et al. J. Comput. Chem. 26, 1668–1688 (2005).

    Article  CAS  Google Scholar 

  13. Todorov, I. T., Smith, W., Trachenko, K. & Dove, M. T. J. Mater. Chem. 16, 1911–1918 (2006).

    Article  CAS  Google Scholar 

  14. Abraham, M. J. et al. SoftwareX 1–2, 19–25 (2015).

    Article  Google Scholar 

  15. Plimpton, S. J. Comput. Phys. 117, 1–19 (1995).

    Article  CAS  Google Scholar 

  16. Phillips, J. C. et al. J. Comput. Chem. 26, 1781–1802 (2005).

    Article  CAS  Google Scholar 

  17. Eastman, P. et al. PLoS Comput. Biol. 13, e1005659 (2017).

    Article  Google Scholar 

  18. Hutter, J., Iannuzzi, M., Schiffmann, F. & VandeVondele, J. Wiley Interdiscip. Rev. Comput. Mol. Sci. 4, 15–25 (2013).

    Article  Google Scholar 

  19. Ceriotti, M., More, J. & Manolopoulos, D. E. Comput. Phys. Commun. 185, 1019–1026 (2014).

    Article  CAS  Google Scholar 

  20. Tuckerman, M. E., Yarne, D. A., Samuelson, S. O., Hughes, A. L. & Martyna, G. J. Comput. Phys. Commun. 128, 333–376 (2000).

    Article  CAS  Google Scholar 

  21. Giannozzi, P. et al. J. Phys. Condens. Matter 21, 395502 (2009).

    Article  Google Scholar 

  22. Giorgino, T. Comput. Phys. Commun. 185, 1109–1114 (2014).

    Article  CAS  Google Scholar 

  23. Doerr, S., Harvey, M. J., Noé, F. & De Fabritiis, G. J. Chem. Theory Comput. 12, 1845–1852 (2016).

    Article  CAS  Google Scholar 

  24. Swenson, D. W. H., Prinz, J.-H., Noé, F., Chodera, J. D. & Bolhuis, P. G. J. Chem. Theory Comput. 15, 813–836 (2019).

    Article  Google Scholar 

  25. Anonymous Nat. Methods 16, 207 (2019).

    Article  Google Scholar 

  26. Valsson, O. & Parrinello, M. Phys. Rev. Lett. 113, 090601 (2014).

    Article  Google Scholar 

  27. Chen, H., Fu, H., Shao, X., Chipot, C. & Cai, W. J. Chem. Inf. Model. 58, 1315–1318 (2018).

    Article  CAS  Google Scholar 

  28. White, A. D. & Voth, G. A. J. Chem. Theory Comput. 10, 3023–3030 (2014).

    Article  CAS  Google Scholar 

  29. Morishita, T., Yonezawa, Y. & Ito, A. M. J. Chem. Theory Comput. 13, 3106–3119 (2017).

    Article  CAS  Google Scholar 

  30. Pipolo, S. et al. Phys. Rev. Lett. 119, 245701 (2017).

    Article  CAS  Google Scholar 

  31. Rydzewski, J. Preprint at https://arxiv.org/abs/1904.03929 (2019).

  32. Bonomi, M. & Camilloni, C. Bioinformatics 33, 3999–4000 (2017).

    Article  CAS  Google Scholar 

Download references

Author information

Author notes

  1. Sandip De

    Present address: BASF SE, Ludwigshafen, Germany

Authors and Affiliations

  1. Department of Structural Biology and Chemistry, Institut Pasteur, Paris, France

    Massimiliano Bonomi

  2. UMR 3528, CNRS, Paris, France

    Massimiliano Bonomi

  3. International School for Advanced Studies (SISSA), Trieste, Italy

    Giovanni Bussi, Mattia Bernetti, Andrea Cesari & Alessandro Laio

  4. Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy

    Carlo Camilloni & Cristina Paissoni

  5. Atomistic Simulation Centre, Queen’s University Belfast, Belfast, UK

    Gareth A. Tribello

  6. Faculty of Science, Palacký University, Olomouc, Czech Republic

    Pavel Banáš

  7. Centre de Biochimie Structurale de Montpellier, Montpellier, France

    Alessandro Barducci

  8. UMR 5048, CNRS, Montpellier, France

    Alessandro Barducci

  9. U 1054, INSERM, Montpellier, France

    Alessandro Barducci

  10. Université de Montpellier, Montpellier, France

    Alessandro Barducci

  11. Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, the Netherlands

    Peter G. Bolhuis & Bernd Ensing

  12. Italian Institute of Technology, Genova, Italy

    Sandro Bottaro & Michele Parrinello

  13. Schrödinger Inc., Cambridge, UK

    Davide Branduardi

  14. Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich, Jülich, Germany

    Riccardo Capelli & Paolo Carloni

  15. Institute of Materials, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland

    Michele Ceriotti & Federico Giberti

  16. National Centre for Computational Design and Discovery of Novel Materials (MARVEL), Lausanne, Switzerland

    Michele Ceriotti & Federico Giberti

  17. Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, China

    Haochuan Chen & Haohao Fu

  18. Department of Physics, University of Illinois, Urbana-Champaign, Urbana, IL, USA

    Wei Chen

  19. Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain

    Francesco Colizzi

  20. Institute of Materials, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland

    Sandip De

  21. Pawsey Supercomputing Centre, Kensington, Western Australia, Australia

    Marco De La Pierre

  22. Department of Chemistry, University of California, Davis, Davis, CA, USA

    Davide Donadio

  23. Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia

    Viktor Drobot

  24. Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA

    Andrew L. Ferguson

  25. Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA

    Marta Filizola & Davide Provasi

  26. Department of Bioengineering and Therapeutic Science, University of California, San Francisco, San Francisco, CA, USA

    James S. Fraser

  27. California Institute for Quantitative Biology, University of California, San Francisco, San Francisco, CA, USA

    James S. Fraser

  28. Department of Physics and Astronomy, University College London, London, UK

    Piero Gasparotto & Angelos Michaelides

  29. Thomas Young Centre, London, UK

    Piero Gasparotto, Angelos Michaelides & Matteo Salvalaglio

  30. Department of Chemistry, University College London, London, UK

    Francesco Luigi Gervasio

  31. Institute of Structural and Molecular Biology, University College London, London, UK

    Francesco Luigi Gervasio

  32. National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA

    Alejandro Gil-Ley & Fabrizio Marinelli

  33. Biophysics Institute (IBF-CNR), National Research Council, Milan, Italy

    Toni Giorgino

  34. Department of Chemistry, University of Cambridge, Cambridge, UK

    Gabriella T. Heller, Thomas Löhr & Michele Vendruscolo

  35. Department of Chemistry, New York University, New York, NY, USA

    Glen M. Hocky

  36. Department of Chemistry, University of Zurich, Zurich, Switzerland

    Marcella Iannuzzi

  37. Department of Physics, ETH Zurich, Lugano, Switzerland

    Michele Invernizzi

  38. Faculty of Informatics, Università della Svizzera italiana, Lugano, Switzerland

    Michele Invernizzi, Michele Parrinello, Pablo Piaggi & GiovanniMaria Piccini

  39. Department of Chemistry, Imperial College London, London, UK

    Kim E. Jelfs

  40. Department of Chemistry, Technical University of Munich, Garching, Germany

    Alexander Jussupow

  41. Institute of Advanced Study, Technical University of Munich, Garching, Germany

    Alexander Jussupow

  42. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia

    Evgeny Kirilin

  43. International Centre for Theoretical Physics (ICTP), Trieste, Italy

    Alessandro Laio

  44. Faculty of Biomedical Sciences, Institute of Computational Science, Università della Svizzera italiana, Lugano, Switzerland

    Vittorio Limongelli & Stefano Raniolo

  45. Department of Pharmacy, University of Naples “Federico II,”, Naples, Italy

    Vittorio Limongelli

  46. Department of Biology, University of Copenhagen, Copenhagen, Denmark

    Kresten Lindorff-Larsen

  47. CNR-IOM/Democritos National Simulation Center, Istituto Officina dei Materiali, Trieste, Italy

    Layla Martin-Samos

  48. Department of Pharmacy and Biotechnology, Alma Mater Studiorum–University of Bologna, Bologna, Italy

    Matteo Masetti

  49. Institute of Experimental Physics, Graz University of Technology, Graz, Austria

    Ralf Meyer

  50. Physics Department, King’s College London, London, UK

    Carla Molteni

  51. CD-FMat, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan

    Tetsuya Morishita

  52. Department of Chemistry, University of Illinois, Urbana-Champaign, Urbana, IL, USA

    Marco Nava

  53. Danish Cancer Society Research Center, Copenhagen, Denmark

    Elena Papaleo

  54. Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark

    Elena Papaleo

  55. Department of Chemistry and Applied Biosciences, ETH Zurich, Lugano, Switzerland

    Michele Parrinello, Pablo Piaggi & GiovanniMaria Piccini

  56. Department of Chemical Engineering, University of Washington, Seattle, WA, USA

    Jim Pfaendtner

  57. Dipartimento di Scienze della Salute, University of Catanzaro, Catanzaro, Italy

    Adriana Pietropaolo

  58. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, Paris, France

    Fabio Pietrucci

  59. UMR 7590 CNRS, Paris, France

    Fabio Pietrucci

  60. Muséum National d’Histoire Naturelle, Paris, France

    Fabio Pietrucci

  61. Department of Chemistry, Université de Lille, Lille, France

    Silvio Pipolo

  62. UMR 8181, CNRS, Lille, France

    Silvio Pipolo

  63. Department of Physics, University of Warwick, Coventry, UK

    David Quigley

  64. School of Life and Molecular Sciences, Curtin University, Perth, Western Australia, Australia

    Paolo Raiteri

  65. Curtin Institute for Computation, Curtin University, Perth, Western Australia, Australia

    Paolo Raiteri

  66. Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Torun, Poland

    Jakub Rydzewski

  67. Department of Chemical Engineering, University College London, London, UK

    Matteo Salvalaglio

  68. Department of Chemistry, University of Warwick, Coventry, UK

    Gabriele Cesare Sosso

  69. Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic

    Vojtěch Spiwok

  70. Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic

    Jiří Šponer

  71. Centre Blaise Pascal, École Normal Supérieure de Lyon, Lyon, France

    David W. H. Swenson

  72. Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA

    Pratyush Tiwary

  73. Institute for Physical Science and Technology, University of Maryland, College Park, MD, USA

    Pratyush Tiwary

  74. Max Planck Institute for Polymer Research, Mainz, Germany

    Omar Valsson

  75. Department of Chemistry, the University of Chicago, Chicago, IL, USA

    Gregory A. Voth

  76. Department of Chemical Engineering, University of Rochester, Rochester, NY, USA

    Andrew White

Consortia

The PLUMED consortium

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

Contributions

All members of the PLUMED consortium contributed to writing of the manuscript.

Corresponding authors

Correspondence to Massimiliano Bonomi, Giovanni Bussi, Carlo Camilloni or Gareth A. Tribello.

Ethics declarations

Competing interests

G.M.H. is currently consulting on a US Department of Energy grant to Parallel Works, Inc.

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The PLUMED consortium. Promoting transparency and reproducibility in enhanced molecular simulations. Nat Methods 16, 670–673 (2019). https://doi.org/10.1038/s41592-019-0506-8

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