/basic_simulation_training

A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations (oriented towards molecular dynamics (MD)), providing some training itself and linking out to other helpful information elsewhere. The intent is that this provide information on the prerequisites which will be required for understanding/following many of the other "best practices" documents being prepared.

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Basic Simulation Training

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.

List of Authors

(Add your name here if you help write; needs updating with list of people who contributed to outline)

  • Avisek Das (University of Michigan)
  • David Mobley (UC Irvine)
  • Jacob Monroe (UC Santa Barbara)
  • Justin Gilmer (Vanderbilt University)

List of Contributors

(Needs updating with everyone who provides input; should also list exactly what people did.)

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

Changelog

  • Sept. 8, 2017: D. Mobley created repo, put in initial files from LiveCoMS.