Promoting transparency and reproducibility in enhanced molecular simulations

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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.

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References

  1. 1.

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

  2. 2.

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

  3. 3.

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

  4. 4.

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

  5. 5.

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

  6. 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. 7.

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

  8. 8.

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

  9. 9.

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

  10. 10.

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

  11. 11.

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

  12. 12.

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

  13. 13.

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

  14. 14.

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

  15. 15.

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

  16. 16.

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

  17. 17.

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

  18. 18.

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

  19. 19.

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

  20. 20.

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

  21. 21.

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

  22. 22.

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

  23. 23.

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

  24. 24.

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

  25. 25.

    Anonymous Nat. Methods 16, 207 (2019).

  26. 26.

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

  27. 27.

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

  28. 28.

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

  29. 29.

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

  30. 30.

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

  31. 31.

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

  32. 32.

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

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Author information

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

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

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Competing interests

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

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