merge upstream

Author: justinGilmer

paper/basic_training.pdf

@@ -16,7 +16,7 @@
 \usepackage{siunitx}
 \DeclareSIUnit\Molar{M}
 \usepackage[italic]{mathastext}
-\newcommand{\versionnumber}{0.1}  % you should update the minor version number in preprints and major version number of submissions.
+\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/MobleyLab/basic_simulation_training}}  %this should be the main github repository for this article
 \graphicspath{{figures/}}
 
@@ -52,22 +52,18 @@
 \affil[4]{University of California, Irvine}
 \affil[5]{University of California, Santa Barbara}
 \affil[6]{National Institutes of Health}
+\affil[6]{Johns Hopkins University, Baltimore}
 \affil[7]{Oregon Health and Science University}
 
 
-\corr{[email protected] }{EB}  % Correspondence emails.  FMS and FS are the appropriate authors initials.
+\corr{[email protected] }{EB}  
 \corr{[email protected]}{JG}
 \corr{[email protected]}{HM}
 \corr{[email protected]}{DLM}
 \corr{[email protected]}{JIM}
-\corr{[email protected]}{SP}
+\corr{[email protected]}{SP}
 \corr{[email protected]}{DMZ}
 
-%\contrib[\authfn{1}]{These authors contributed equally to this work}
-%\contrib[\authfn{2}]{These authors also contributed equally to this work}
-
-%\presentadd[\authfn{3}]{Department, Institute, Country}
-%\presentadd[\authfn{4}]{Department, Institute, Country}
 
 \blurb{This LiveCoMS document is maintained online on GitHub at
 \githubrepository; to provide feedback, suggestions, or help improve it, please
@@ -406,7 +402,7 @@ \subsubsection{Key concepts}
 \begin{figure}[h]
 \centering
 \includegraphics[width=\linewidth]{potentials_basic_horiz.pdf}
-\caption{Standard MM force fields include terms that represent (a) bond and angle stretching around equilibrium values, using harmonic potentials with spring constants fit to the molecules and atoms to which they are applied. (b) Rotation around dihedral angles (green arrow) are defined using four atoms.}
+\caption{Standard MM force fields include terms that represent (a) bond and angle stretching around equilibrium values, using harmonic potentials with spring constants fit to the molecules and atoms to which they are applied; and (b) rotation around dihedral angles (green arrow) defined using four atoms, typically using a cosine expansion.}
 \label{potentials}
 \end{figure}
 
@@ -523,7 +519,7 @@ \subsection{Periodic boundary conditions}
 \begin{figure}[h]
 \centering
 \includegraphics[width=\linewidth]{PBC_figure.pdf}
-\caption{Periodic boundary conditions are shown for a simple 2D system. Note that the simulated system is a sub-ensemble within an infinitely sized system of identical, small ensembles.}
+\caption{Periodic boundary conditions are shown for a simple 2D system. Note that the simulated system is a sub-ensemble within an infinite system of identical, small ensembles.}
 \label{pbcfig}
 \end{figure}
 
@@ -639,11 +635,12 @@ \subsubsection{Equilibration}
 \begin{figure}[h]
 \centering
 \includegraphics[width=\linewidth]{Equilibration_fig.png}
-\caption{For some system properties, equilibration may be relatively rapid (top panel), while for others it may be much slower (bottom panel). If it there is ambiguity as to whether or not a key property is still systematically changing, as in the bottom panel, equilibration should be extended.}
+\caption{Shown are graphs of a hypothetical computed property (vertical axis) versus simulation time (horizontal axis). For some system properties, equilibration may be relatively rapid (top panel), while for others it may be much slower (bottom panel). If it there is ambiguity as to whether or not a key property is still systematically changing, as in the bottom panel, equilibration should be extended.}
 \label{equilibration}
 \end{figure}
 
 Once the kinetic and potential energies fluctuate around constant values and other key properties are no longer changing with time, the equilibration period has reached its end.
+In general, if any observed properties still exhibit a systematic trend with respect to simulation time (e.g. Figure~\ref{equilibration}) this should be taken as a sign that equilibration is not yet complete.
 
 Depending on the target ensemble for production, the procedure for the end of equilibration is somewhat different.
 If an NVE simulation is desired, the thermostat may be removed and a snapshot selected that is simultaneously as close to the average kinetic and potential energies as possible.
@@ -895,7 +892,7 @@ \subsubsection{Popular Barostats}
     \item \textbf{Martyna-Tuckerman-Tobias-Klein (MTTK)}
 
         The MTTK barostat has substantial similarity to the Parrinello-Rahman and Andersen barostats.
-        When Parrinello-Rahman's equations of motion were discovered to only hold true in the limit of large systems, the MTTK barostat introduced alternate equations of motion to correctly sample the ensemble for smaller systems as well~\cite{martyna1994constant, martyna1996explicit}.
+        When Parr\-inello-Rah\-man's equations of motion were discovered to only hold true in the limit of large systems, the MTTK barostat introduced alternate equations of motion to correctly sample the ensemble for smaller systems as well~\cite{martyna1994constant, martyna1996explicit}.
         Thus, MTTK~\cite{martyna1994constant, martyna1996explicit} is usually seen as an improvement over Parrinello-Rahman~\cite{Parrinello1981} for such systems.
 
     \item \textbf{Monte Carlo}
@@ -1058,18 +1055,18 @@ \subsubsection{ Ewald Summation}
 \centering
 \includegraphics[width=\linewidth]{ewald.pdf}
 
-    \caption{\label{fig:screening}Screening charge distribution. (top) Original charge distribution. (bottom) Point charges can be split into Direct space(blue) and Reciprocal space charges(red). Direct space charge consists of the original charges and gaussian-distributed screening charge. Reciprocal space charge is only the Gaussian-distributed charge. }
+    \caption{\label{fig:screening}Screening charge distribution. (Top) The original charge distribution. (Bottom) Point charges can be split into Direct space (blue) and Reciprocal space charges (red). The direct space charge consists of the original charges and Gaussian-distributed screening charges of opposite sign. The reciprocal space charge is only the Gaussian-distributed charge of the original sign. Together these sum to the original charge distribution, but computation of the electrostatic potential due to each component becomes much easier.}
 \label{charges_ewald}
 \end{figure}
 
-Unlike the original, full potential, the direct space screened interaction (Figure~\ref{fig:screening}, top) decays rapidly (Figure~\ref{fig:charges_ewald}).
-In fact, it decays even faster than Van der Waals interactions ($1/r^{6}$) and hence relative short cutoffs, comparable to those used for Van der Waals interactions, can be used for handling direct-space Coulomb interactions.
+Unlike the original, full potential, the direct space screened interaction (Figure~\ref{fig:screening}, top) decays rapidly .
+In fact, it decays even faster than van der Waals interactions ($1/r^{6}$) and hence relative short cutoffs, comparable to those used for van der Waals interactions, can be used for handling direct-space Coulomb interactions (Figure~\ref{decay}).
 
 
 \begin{figure}[h]
 \centering
 \includegraphics[width=\linewidth]{decay_comparison.pdf}
-    \caption{Comparison of decay of original $r^{-1}$ term(blue,*), erfc(r) in direct space(black,-) and $r^{-6}$ in van der waals term (red, -.).  }
+    \caption{Comparison of decay of the original $r^{-1}$ term for Coulomb interactions (blue,*), the resulting direct-space term after Gaussian screening (black,-) and the $r^{-6}$ in van der Waals term (red, -.).  }
 \label{decay}
 \end{figure}
 
@@ -1098,9 +1095,7 @@ \subsubsection{Grid based Ewald summation}
 
 \item Transformation of the grid to reciprocal space: A Fast Fourier Transform (FFT) is used to convert the charges on the grid to their equivalent Fourier space structure factors.
 
-\item Energy calculation: The reciprocal space potential is calculated by solving the Poisson equation in Fourier space. At the same time, the grid is modified to store the reciprocal space potential. 
-\todo[inline, color={yellow!20}]{DLM: What does ``the grid is modified'' mean here and is it important? Does this mean just that the potential is stored at for each grid point?}
-
+\item Energy calculation: The reciprocal space potential is calculated by solving the Poisson equation in Fourier space, and the reciprocal space potential is then stored on the grid.
 
 \item Transformation of the grid back to real space: An Inverse FFT is used to convert the reciprocal space potential back to the real space. 
 \item Force calculation: The force is given by the gradient of the potential.
@@ -1238,7 +1233,7 @@ \section{Conclusions}
 
 Our focus here has been on the basics --- focusing on things you need to understand before beginning to prepare simulations for yourself.
 Additionally, we have primarily focused on issues relating to how simulations are conducted, and leave data analysis for a separate treatment.
-As a starting point relating to data analysis, readers should probably review the Best Practices document on sampling and uncertainty estimation (\url{https://github.com/dmzuckerman/Sampling-Uncertainty})).
+As a starting point relating to data analysis, readers should probably review the Best Practices document on sampling and uncertainty estimation (\url{https://github.com/dmzuckerman/Sampling-Uncertainty}).
 
 Please remember that this is an updatable work, so we welcome contributions and suggestions via our GitHub issue tracker so that we can make this a valuable resource for the field which clearly addresses the key fundamentals.