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Best Practices for Alchemical Free Energy Simulations

v2.0 Update

The original best practices guide will be split into two documents: the first will gives best practices for running a single calculation (and give details on theory/ system-specific setup), while the second will give best practices for running multiple calculations (with a focus on automation). The first (this manuscript) will become version 2.0 of the current guide, while the second will be submitted as a new manuscript (see this repo).

Goals

  • Checklist and background for new practitioners of relative and absolute alchemical free energy calculations: What should you pay attention to in setting up and running calculations in common codes and why.
  • Provide guidance to authors as to what should be reported about their protocols in a Methods section, either conforming to standard or reporting where they did not conform and why. Useful to reviewers as well.

Scope

Preparation (focused on aspects unique to alchemical free energies), execution, and analysis of:

  • Transfer free energies (hydration free energies, partition coefficients, etc.)
  • Binding free energies

List of Authors

(As ordered on the paper)

  • Antonia S. J. S. Mey
  • Bryce Allen
  • Hannah E. Bruce Macdonald
  • John D. Chodera
  • David F. Hahn
  • Maximilian Kuhn
  • Julien Michel
  • David L. Mobley
  • Levi N. Naden
  • Samarjeet Prasad
  • Andrea Rizzi
  • Jenke Scheen
  • Michael R. Shirts
  • Gary Tresadern
  • Huafeng Xu

List of Contributors

(non-author list of people who contributed to document)

  • Julia Rice -- Attended initial discussion meeting at NIST in Aug. 2017

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.

Online Resources

Original brainstorming document: (https://docs.google.com/document/d/1h7GIyOJykBWz-GPKtYZK-Pv7cbLbX8XTM2xLUpSppoE)

List of Released Versions

revisions for v 1.0