Best Practices Guides

What is a best practices guide?

The goal of best practices manuscripts are to improve the quality of simulation research by providing advice that can eliminate the most common errors.

These documents consist of:

A. A checklist: A succinct list of steps that people should follow when carrying out the task in question. This is provided to ensure certain basic standards are followed and common but critical major errors are avoided.

B. The rationale: A much more detailed section with the necessary rationale for the checklist, which would act as more complete best practices description. This should include 1) significant detail as to the possible alternative ways to accomplish a given task, 2) description of advantages and disadvantages of the various approaches, and 3) significant literature documentation about reasons for choices.

The inspiration for best practices guides can be found in the Atul Gawande article The Checklist, later expanded in his bestseller The Checklist Manifesto. The main goal of these documents is to reduce common errors by ensuring appropriate choices are made throughout a difficult task.

For our purposes, simulation checklists should help users avoid the most common reasons for failure or incorrect results. Checklists will typically also be accompanied by a detailed explanation with sources and references (the rationale mentioned above), and this rationale can go into more detail on best practices and cover more possible failure modes and how to avoid them.

One can divide the types of errors that are made performing molecular simulations into (a) mistakes experienced researchers often make, (b) mistakes new users often make despite having received solid training in the fundamentals of molecular simulation, and (c) mistakes made due to lack of or poor training. Checklists in this journal will typically focus on errors that are likely to be made by users with training and experience in molecular simulations, i.e., errors of type (a) and (b). As such, normal best practices documents can and should assume a basic familiarity with the fundamentals of molecular simulations.

Additional criteria considered in reviews of best practices guides

Reviewers will consider the following factors in reviewing best practices guides:

  • Would following the provided checklist help users avoid significant potential errors in simulation? Will the errors be profound and/or frequent?
  • Are all assertions well-sourced in published data (which may, in some cases, include data created for the paper)?
  • Are the explanations clear enough for researchers with only moderate training in simulation?

Revision schedule for best practices guides

Best practices guides may start with more frequent versions, as initial rounds of community input are solicited. As always, authors are encouraged to update their private GitHub versions as frequently as desired, and if the document changes rapidly, more frequent new versions on LiveCoMS may be needed; consultation with your editor is encouraged.