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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 …

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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 when it is available.

List of Authors

  • 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)

List of Contributors

  • Avisek Das (helped with outline and early brainstorming/planning of this document)
  • Victoria Tran Lim provided valuable editorial feedback on the document
  • Michael Shirts caught a variety of typos and other minor issues, and suggested some improvements.
  • Emmanuel Karagiorgos caught some duplicated references

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

Citing this work

Version 1.0 of this work is being published in the Living Journal of Computaitonal Molecular Science (LiveCoMS) volume 1, issue 1, page/article 5957 (2019). It is available at this DOI: 10.33011/livecoms.1.1.5957.

Ongoing (non-peer reviewed) versions of this article will be assigned unique DOIs via Zenodo which will be posted here and can be cited by these DOIs; subsequent peer reviewed versions (when applicable) are planned to be published in LiveCoMS.

Changelog

  • 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.
  • Nov. 23, 2018: Check references using fixbibtex, incorporate fixes for problems it caught; addresses a number of typos/missing references caught by Michael Shirts.
  • Nov. 28, 2018: Add DOI, include citation to Grossfield et al. LiveCoMS article with DOI.
  • Dec. 18, 2018: Fix duplicated references.
  • Dec. 29, 2018: Finalize formatting for publication.

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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 …

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