Enhanced Sampling Methods for Molecular Dynamics Simulations

A repository for a LiveCoMS Perpetual Review on enhanced sampling methods titled "Enhanced Sampling Methods for Molecular Dynamics Simulations". Version 1.0 published in LiveCoMS under DOI: 10.33011/livecoms.4.1.1583.

List of Authors

• Jérôme Hénin, Laboratoire de Biochimie Théorique UPR 9080, CNRS, Université de Paris, Paris, France, and Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, Paris, France
• Tony Lelièvre, CERMICS, Ecole des Ponts, INRIA, Marne-la-Vallée, France
• Michael R. Shirts, Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
• Omar Valsson, University of North Texas, Department of Chemistry, Denton, TX, USA
• Lucie Delemotte, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden

Citation

Please use the following citation for the review:

Hénin, J. ., Lelièvre, T., Shirts, M. R., Valsson, O., & Delemotte, L. (2022). Enhanced Sampling Methods for Molecular Dynamics Simulations [Article v1.0]. Living Journal of Computational Molecular Science, 4(1), 1583. https://doi.org/10.33011/livecoms.4.1.1583

Or in BibTeX format:

@article{Henin_Lelievre_Shirts_Valsson_Delemotte_2022, 
         place={Boulder, CO, USA}, 
         author={H{\'e}nin, J{\'e}r{\^o}me and Leli{\`e}vre, Tony and Shirts, Michael R. and Valsson, Omar and Delemotte, Lucie}, 
         title={Enhanced Sampling Methods for Molecular Dynamics Simulations [Article v1.0]}, 
         journal={Living Journal of Computational Molecular Science}, 
         volume={4}, 
         number={1}, 
         year={2022}, 
         month={Dec.}, 
         pages={1583},
         url={https://livecomsjournal.org/index.php/livecoms/article/view/v4i1e1583}, 
         DOI={10.33011/livecoms.4.1.1583}
         }

List of Contributors

Paper writing as code development

This paper is being developed as a living document, open to changes from the community. You can read more about the concept of writing a paper in the same way one would write software code in the essay "Paper writing as code development". If you have comments or suggestions, we welcome them! Please submit them as issues to this GitHub repository so they can be recorded and given credit for the contribution. Specific changes can be proposed via pull requests.

List of Released Versions

• v0.5: Initial submisson to LiveCoMS, and posted on arXiv.
• v0.7: Revised submisson to LiveCoMS, and posted on arXiv.
• v1.0: Published version in LiveCoMs, and posted under DOI: 10.33011/livecoms.4.1.1583.

Changelog

• 9 February 2022: Version v0.5 submitted to LiveCoMS, and posted on arXiv.
• 19 August 2022: Version v0.7 (revision) submitted to LiveCoMS, and posted on arXiv.
• 14 December 2022: Version v1.0 published in LiveCoMS, and posted under DOI: 10.33011/livecoms.4.1.1583.