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main.tex
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% LIVECOMS ARTICLE TEMPLATE FOR BEST PRACTICES GUIDE
%%% ADAPTED FROM ELIFE ARTICLE TEMPLATE (8/10/2017)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% PREAMBLE
\documentclass[9pt,bestpractices,pubversion]{livecoms}
% Use the 'onehalfspacing' option for 1.5 line spacing
% Use the 'doublespacing' option for 2.0 line spacing
% Use the 'lineno' option for adding line numbers.
% The 'bestpractices' option for indicates that this is a best practices guide.
% Omit the bestpractices option to remove the marking as a LiveCoMS paper.
% Please note that these options may affect formatting.
\usepackage{lipsum} % Required to insert dummy text
\usepackage[version=4]{mhchem}
\usepackage{siunitx}
\usepackage{bm}
\DeclareSIUnit\Molar{M}
\usepackage[italic]{mathastext}
\newcommand{\versionnumber}{1.0} % you should update the minor version number in preprints and major version number of submissions.
\newcommand{\githubrepository}{\url{https://github.com/dmzuckerman/Sampling-Uncertainty}} %this should be the main github repository for this article
\graphicspath{{figures/}}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% ARTICLE SETUP
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\title{Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations [Article v\versionnumber]}
\author[1*\authfn{1}]{Alan Grossfield}
\author[2*\authfn{1}]{Paul N. Patrone}
\author[3*\authfn{1}]{Daniel R. Roe}
\author[4*\authfn{1}]{Andrew J. Schultz}
\author[5*\authfn{1}]{Daniel W. Siderius}
\author[6*\authfn{1}]{Daniel M. Zuckerman}
\affil[1]{University of Rochester Medical Center, Department of Biochemistry and Biophysics}
\affil[2]{Applied Computational and Mathematics Division, National Institute of Standards and Technology}
\affil[3]{Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health}
\affil[4]{Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York}
\affil[5]{Chemical Sciences Division, National Institute of Standards and Technology}
\affil[6]{Department of Biomedical Engineering, Oregon Health \& Science University}
\corr{[email protected]}{AG}
\corr{[email protected]}{PNP}
\corr{[email protected]}{DRR}
\corr{[email protected]}{AJS}
\corr{[email protected]}{DWS}
\corr{[email protected]}{DMZ}
\orcid{Alan Grossfield}{0000-0002-5877-2789}
\orcid{Paul N. Patrone}{0000-0002-9446-8186}
\orcid{Daniel R. Roe}{0000-0002-5834-2447}
\orcid{Andrew J. Schultz}{0000-0002-1180-0156}
\orcid{Daniel W. Siderius}{0000-0002-6260-7727}
\orcid{Daniel M. Zuckerman}{0000-0001-7662-2031}
\contrib[\authfn{1}]{These authors contributed equally to this work.}
\blurb{This LiveCoMS document is maintained online on GitHub at \githubrepository; to provide feedback, suggestions, or help improve it, please visit the GitHub repository and participate via the issue tracker.\\
\bigskip
Contribution of the National Institute of Standards and Technology, not subject to US copyright.
}
%% Common symbols
\newcommand{\stdev}[1]{s\left( #1 \right)}
\newcommand{\stdevmean}[1]{s\left( #1 \right)}
\newcommand{\expval}[1]{\langle #1 \rangle}
\newcommand{\mean}[1]{\bar{#1}}
\newcommand{\expvar}[1]{\sigma_{#1}^2}
\newcommand{\var}[1]{s^2\left( #1 \right)}
%\presentadd[\authfn{3}]{Department, Institute, Country}
%\presentadd[\authfn{4}]{Department, Institute, Country}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% PUBLICATION INFORMATION
%%% Fill out these parameters when available
%%% These are used when the "pubversion" option is invoked
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\pubDOI{10.33011/livecoms.1.1.5067}
\pubvolume{1}
\pubissue{1}
\pubyear{2019}
\articlenum{5067}
\datereceived{20 June 2018}
\dateaccepted{17 October 2018}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% ARTICLE START
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{document}
\begin{frontmatter} %NOTE: to make the document single column, just take out the {frontmatter} sentinels
\maketitle
\begin{abstract}
The quantitative assessment of uncertainty and sampling quality is essential in molecular simulation.
Many systems of interest are highly complex, often at the edge of current computational capabilities. Modelers must therefore analyze and communicate statistical uncertainties so that ``consumers'' of simulated data understand its significance and limitations. This article covers key analyses appropriate for trajectory data generated by conventional simulation methods such as molecular dynamics and (single Markov chain) Monte Carlo. It also provides guidance for analyzing some `enhanced' sampling approaches. We do not discuss \emph{systematic} errors arising, e.g., from inaccuracy in the chosen model or force field.
\end{abstract}
\end{frontmatter}
\section{Introduction: Scope and definitions}
\label{sec:scope}
\input{scope}
\input{definitions}
\input{checklist.tex}
\input{pre-sim-sanity.tex}
\input{quick-and-dirty.tex}
\input{equilibration-burn-in.tex}
\input{global-sampling.tex}
\input{specific-observables.tex}
\input{enhanced-sampling.tex}
\input{conclusion.tex}
\section*{Acknowledgments}
The authors appreciate helpful discussions with Pascal T. Merz (University of Colorado-Boulder), comments on the text from John Chodera (Memorial Sloan Kettering Cancer Center), Lillian T.~Chong (University of Pittsburgh) and William R.~Smith (University of Guelph), and valuable feedback from Harold W.~Hatch, Richard A.~Messerly, Raymond D.~Mountain, and Andrew M.~Dienstfrey in their roles as NIST reviewers.
DMZ acknowledges support from NIH Grant GM115805.
\section*{Disclaimer}
Certain commercially available items may be identified in this paper. This identification does not imply recommendation by NIST, nor does it imply that it is the best available for the purposes described.
\section*{Author Information}
\makeorcid
\bibliography{refs}
\end{document}