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From Proteins to Perturbed Hamiltonians: A Suite of Tutorials for the GROMACS-2018 Molecular Simulation Package

This document contains a description of seven tutorials for carrying out different types of molecular dynamics (MD) simulations in the popular, open-source GROMACS package.

List of Authors

  • Justin A. Lemkul, Virginia Tech, Blacksburg, VA, USA

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

  • v1.0: Submitted to LiveCoMS


  • 5 March 2018: Started document
  • 10 July 2018: First full draft completed, all tutorials updated for GROMACS-2018
  • 27 August 2018: Revised based on peer review comments
  • 10 September 2018: Revised based on editorial comments
  • 30 December 2018: Final version of PDF and article files for publication in LiveCoMS
  • 2 January 2019: Final formatting fixes