Best Practices article intended for LiveCoMS
Clone or download
Permalink
Failed to load latest commit information.
Cover_Art Added PNG format cover art Jun 26, 2018
Revision_1 Adding Diff and Response Letter for Revised Submission Aug 29, 2018
Revision_2 Adding Diff and Response Letter for Revised Submission #2 Oct 16, 2018
figures Moved graphic to figures May 31, 2018
.gitignore Updated git ignore Jun 19, 2018
Metrology_Vocabulary_JCGM_200_2012.pdf Added VIM to repo for reference. Oct 12, 2017
README.md update README for article acceptance date Oct 19, 2018
Uncertainty_Guide_JCGM_100_2008_E.1-dmz.pdf VIM uncertainty guide with highlighting Oct 4, 2017
checklist.tex Changed wording re publication of data to more strongly encourage it Aug 24, 2018
conclusion.tex removed comments and commented-out lines Jun 5, 2018
definitions.tex Fixed footnote location per editor instructions Oct 18, 2018
enhanced-sampling.tex Fixed a few abbreviations for eq, sec, etc. and recompiled Aug 28, 2018
equilibration-burn-in.tex Grammar/wording revisions based on review round 2 Sep 26, 2018
from-google-doc.md Update from-google-doc.md Aug 28, 2017
global-sampling.tex DMZ minor edits to global section Aug 27, 2018
livecoms.cls Updated class file Oct 12, 2018
main.pdf Fixed footnote location per editor instructions Oct 18, 2018
main.tex Updated table format to [Article v1.0] type Oct 10, 2018
pre-sim-sanity.tex Reviewed hyphenation and made corrections May 31, 2018
quick-and-dirty.tex Fixed index in equation 10 and recompiled PDF Oct 12, 2018
refs.bib Fixed references, updated bibliography, recompiled PDF Oct 5, 2018
scope.tex DMZ added ref to Nicholls UQ paper Aug 27, 2018
specific-observables.tex converted eq 10 to proper ACF definition, then referenced it in secti… Oct 11, 2018
vancouver-livecoms.bst Updated class file, bibtex style, added publication date macros, and … Jul 9, 2018

README.md

Sampling-Uncertainty

Best Practices article for LiveCoMS (Living Journal of Computational Molecular Science) [http://www.livecomsjournal.org/] ACCEPTED ON 17 OCT 2018

This is an article motivated by the Best Practices workshop organized by Michael Shirts on behalf of MolSSI, held at NIST on Aug 24-25, 2017.

The article is intended as a guide for beginning molecular simulators (and beyond) to understand and assess sampling quality, 'convergence', and statistical uncertainty.

Comments and suggestions from the community are welcomed. It is hoped that this article will be regularly updated to maximize its utility for the community. Significant contributions will be considered as a potential basis for authorhsip.

The initial draft scope of the article: This article is geared toward studies attempting to quantify observables and derive reliable error bars based on “standard” canonical sampling methods (e.g., molecular dynamics and Monte Carlo) and associated “enhanced” sampling methods. Some problems and systems may be better studied with cruder techniques and analyses, which will not be covered here.