Best Practices document to be submitted to the Living Journal of Computational Molecular Science
This repository contains a document (and supporting materials) to lay out best practices in calculating free energy profiles and potentials of mean force from molecular dynamics simulations. This is a broad topic, and we do not aim to provide an in-depth review of all methods and approaches. Rather, we aim to provide a concise document that highlights especially key points and pitfalls, with references to some of the many fine sources available to gain further knowledge.
(Add your name here if you help write this article)
- Alan Grossfield (UC Irvine)
- Heather Mayes (University of Michigan)
Invited authors to contribute soon:
- Anthony Hazel
- Michael Shirts
- Sunny Hwang
- Alan Grossfield
- Baron Peters
- Jon Whitmer
- Andrew Ferguson
People to invite: Francesco Gervasio
This is intended to be a sample of workflow for designing a free energy curve / PMF calculation. It cannot be comprehensive, as it is intended to be just one article (approx. 12 pages). Think of this as a "quick-start" guide to express key concepts, with references to other sources for further information.
We developed an outline, which is now part of the latex document in this repository. If you would like to work on a section, please put your name in comments near the section or subsection title (see examples in the tex file). You are welcome to work on latex "subfiles", as Alan Grossfield has, or directly in the main document ("best_pmf.tex"). As discussed below, all contributions will be reviewed through pull requests, as well as sign-off from authors before submission.
As copied from other LiveCoMS efforts: 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.