Merge pull request #74 from MobleyLab/hbmayes

Add new figure on terms in energy function

Author: davidlmobley

.gitignore

@@ -179,3 +179,5 @@ TSWLatexianTemp*
 
 # KBibTeX
 *~[0-9]*
+
+temp_graphic_files

paper/basic_training.pdf

@@ -99,7 +99,7 @@ \section{Introduction}
 
 Molecular simulation techniques play a very important role in our quest to understand and predict the properties, structure, and function of molecular systems, and are a key tool as we seek to enable predictive molecular design.
 Simulation methods are extremely useful for studying the structure and dynamics of complex systems that are too complicated for pen and paper theory, helping interpret experimental data in terms of molecular motions.
-Additionally, they see increasing use for quantitative prediction of properties of use in molecular design and other applications~\cite{Nussinov2014,Towns2014,Kirchmair2015,Sresht2017,Bottaro2018}.
+Additionally, they are increasingly used for quantitative prediction of properties of use in molecular design and other applications~\cite{Nussinov2014,Towns2014,Kirchmair2015,Sresht2017,Bottaro2018}.
 
 The basic idea of any molecular simulation method is straightforward; a particle-based description of the system under investigation is constructed and then the system is propagated by either deterministic or probabilistic rules to generate a trajectory describing its evolution over the course of the simulation~\cite{Frenkel:2001:,LeachBook}.
 Relevant properties can be calculated for each ``snapshot'' (a stored configuration of the system, also called a ``frame'') and averaged over the the entire trajectory to compute estimates of desired properties.
@@ -403,9 +403,16 @@ \subsubsection{Key concepts}
 While these arise from similar or related physical effects (ultimately all tracing back to QM and the basic laws of physics) they are typically treated in rather distinct manners in molecular simulations so it is important to consider the two categories
 separately.
 
+\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.}
+\label{potentials}
+\end{figure}
+
 %Bonded interactions
 Bonded interactions are those between atoms which are connected, or nearly so, and relating to the bonds connecting these atoms. 
-In typical molecular simulations these consist of bond stretching terms, angle bending terms, and terms describing the rotation of torsional angles. 
+In typical molecular simulations these consist of bond stretching terms, angle bending terms, and terms describing the rotation of torsional angles, as shown in Figure \ref{potentials}. 
 Torsions typically involve four atoms and are often of two types -- ``proper'' torsions, around bonds connecting groups of atoms, and ``improper''
 torsions which involve neighbors of a central atom; these are often used to ensure the appropriate degree of planarity or non-planarity around a particular group (such as planarity of an aromatic ring). 
 It is important to note that the presence of bonded interactions between atoms does not necessarily preclude their also having nonbonded interactions with one another (see discussion of exclusions and 1-4 interactions, below).