This repository contains a document (and supporting materials) on Basic Simulation Training, intending to provide prerequisite information for people who want to begin conducting (bio)molecular simulations, especially Molecular Dynamics (MD). Our focus here is to tell people what they need to know and why, with links/references to suitable training material. Some brief summaries of some of the key concepts may be provided, but as we are not out to write a textbook, a focus is on guiding people to the appropriate materials. The current focus is on MD; Monte Carlo (MC) will be addressed in a separate document which will be linked from here when it is available.
- Efrem Braun (Berkeley)
- Justin Gilmer (Vanderbilt)
- Heather B. Mayes (University of Michigan)
- David L. Mobley (UC Irvine)
- Jacob I. Monroe (UC Santa Barbara)
- Samarjeet Prasad (National Institutes of Health; Johns Hopkins University)
- Daniel M. Zuckerman (Oregon Health and Science University)
- Avisek Das (helped with outline and early brainstorming/planning of this document)
- Victoria Tran Lim provided valuable editorial feedback on the document
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.
- Sept. 8, 2017: D. Mobley created repo, put in initial files from LiveCoMS.
- Spring/early summer 2018: Finalize who will be involved and write/edit first version of the paper
- Sept. 2, 2018: Final draft of version 1 submitted to LiveCoMS
- Nov. 5-6, 2018: Make editorial revisions suggested by peer reviewers and Victoria Lim.