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.
References
Camilloni, C. & Pietrucci, F. Adv. Phys. X 3, 1477531 (2018).
Mittal, S. & Shukla, D. Mol. Simul. 44, 891–904 (2018).
Bottaro, S. & Lindorff-Larsen, K. Science 361, 355–360 (2018).
Grossfield, A. et al. Living J. Comput. Mol. Sci. 1, 5067 (2018).
Recommended data repositories. Scientific Data https://www.nature.com/sdata/policies/repositories (2019).
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).
Bonomi, M. et al. Comput. Phys. Commun. 180, 1961–1972 (2009).
Fiorin, G., Klein, M. L. & Hénin, J. Mol. Phys. 111, 3345–3362 (2013).
Sidky, H. et al. J. Chem. Phys. 148, 044104 (2018).
Tribello, G. A., Bonomi, M., Branduardi, D., Camilloni, C. & Bussi, G. Comput. Phys. Commun. 185, 604–613 (2014).
Harvey, M. J., Giupponi, G. & Fabritiis, G. D. J. Chem. Theory Comput. 5, 1632–1639 (2009).
Case, D. A. et al. J. Comput. Chem. 26, 1668–1688 (2005).
Todorov, I. T., Smith, W., Trachenko, K. & Dove, M. T. J. Mater. Chem. 16, 1911–1918 (2006).
Abraham, M. J. et al. SoftwareX 1–2, 19–25 (2015).
Plimpton, S. J. Comput. Phys. 117, 1–19 (1995).
Phillips, J. C. et al. J. Comput. Chem. 26, 1781–1802 (2005).
Eastman, P. et al. PLoS Comput. Biol. 13, e1005659 (2017).
Hutter, J., Iannuzzi, M., Schiffmann, F. & VandeVondele, J. Wiley Interdiscip. Rev. Comput. Mol. Sci. 4, 15–25 (2013).
Ceriotti, M., More, J. & Manolopoulos, D. E. Comput. Phys. Commun. 185, 1019–1026 (2014).
Tuckerman, M. E., Yarne, D. A., Samuelson, S. O., Hughes, A. L. & Martyna, G. J. Comput. Phys. Commun. 128, 333–376 (2000).
Giannozzi, P. et al. J. Phys. Condens. Matter 21, 395502 (2009).
Giorgino, T. Comput. Phys. Commun. 185, 1109–1114 (2014).
Doerr, S., Harvey, M. J., Noé, F. & De Fabritiis, G. J. Chem. Theory Comput. 12, 1845–1852 (2016).
Swenson, D. W. H., Prinz, J.-H., Noé, F., Chodera, J. D. & Bolhuis, P. G. J. Chem. Theory Comput. 15, 813–836 (2019).
Anonymous Nat. Methods 16, 207 (2019).
Valsson, O. & Parrinello, M. Phys. Rev. Lett. 113, 090601 (2014).
Chen, H., Fu, H., Shao, X., Chipot, C. & Cai, W. J. Chem. Inf. Model. 58, 1315–1318 (2018).
White, A. D. & Voth, G. A. J. Chem. Theory Comput. 10, 3023–3030 (2014).
Morishita, T., Yonezawa, Y. & Ito, A. M. J. Chem. Theory Comput. 13, 3106–3119 (2017).
Pipolo, S. et al. Phys. Rev. Lett. 119, 245701 (2017).
Rydzewski, J. Preprint at https://arxiv.org/abs/1904.03929 (2019).
Bonomi, M. & Camilloni, C. Bioinformatics 33, 3999–4000 (2017).
Author information
Authors and Affiliations
Consortia
Contributions
All members of the PLUMED consortium contributed to writing of the manuscript.
Corresponding authors
Ethics declarations
Competing interests
G.M.H. is currently consulting on a US Department of Energy grant to Parallel Works, Inc.
Rights and permissions
About this article
Cite this article
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
Published:
Issue Date:
DOI: https://doi.org/10.1038/s41592-019-0506-8
- Springer Nature America, Inc.
This article is cited by
-
Preventing lipophilic aggregation in cosolvent molecular dynamics simulations with hydrophobic probes using Plumed Automatic Restraining Tool (PART)
Journal of Cheminformatics (2024)
-
Gas adsorption and framework flexibility of CALF-20 explored via experiments and simulations
Nature Communications (2024)
-
Combining stochastic resetting with Metadynamics to speed-up molecular dynamics simulations
Nature Communications (2024)
-
Inhibition and transport mechanisms of the ABC transporter hMRP5
Nature Communications (2024)
-
Dissecting the mechanism of atlastin-mediated homotypic membrane fusion at the single-molecule level
Nature Communications (2024)