updated images

Author: simongravelle

figures/PEG-in-vacuum.png

@@ -9,7 +9,7 @@ group PEG type C CPos H HC OAlc OE
 
 delete_atoms overlap 2.0 H2O PEG mol yes
 
-dump viz all image 250 myimage-*.ppm type &
+dump viz PEG image 250 myimage-*.ppm type &
  type shiny 0.1 box no 0.01 &
  view 0 90 zoom 3 fsaa yes bond atom 0.8 size 1000 500
 dump_modify viz backcolor white &

figures/PEG-in-water.png

@@ -1902,8 +1902,9 @@ \subsubsection{Solvating the PEG in water}
 
 \begin{figure}
 \centering
-\includegraphics[width=\linewidth]{PEG-in-vacuum}
-\caption{The PEG molecule in vacuum. The carbon atoms are in gray, the oxygen
+\includegraphics[width=0.45\linewidth]{PEG-in-vacuum}
+\caption{The PEG molecule from \hyperref[all-atom-label]{Tutorial 3}.
+The carbon atoms are in gray, the oxygen
 atoms in red, and the hydrogen atoms in white.}
 \label{fig:PEG-in-vacuum}
 \end{figure}
@@ -1989,8 +1990,8 @@ \subsubsection{Solvating the PEG in water}
 \begin{figure}
 \centering
 \includegraphics[width=\linewidth]{PEG-solvated}
-\caption{A single PEG molecule in water.  Water molecules are represented as a
-transparent continuum field for clarity.}
+\caption{The PEG molecule solvated in water as simulated during
+\hyperref[all-atom-label]{Tutorial 3}.}
 \label{fig:PEG-solvated}
 \end{figure}
 
@@ -2094,16 +2095,17 @@ \subsubsection{Stretching the PEG molecule}
 \begin{figure}
 \centering
 \includegraphics[width=\linewidth]{PEG-in-water}
-\caption{PEG molecule stretched along the $x$ direction in water. Water molecules
-are represented as a transparent continuum field for clarity.}
+\caption{PEG molecule stretched along the $x$ direction in water
+as simulated during \hyperref[all-atom-label]{Tutorial 3}.}
 \label{fig:PEG-in-water}
 \end{figure}
 
 \begin{figure}
 \centering
 \includegraphics[width=\linewidth]{PEG-distance}
 \caption{a) Evolution of
-the radius of gyration $R_\text{gyr}$ of the PEG molecule, with the force
+the radius of gyration $R_\text{gyr}$ of the PEG molecule
+from \hyperref[all-atom-label]{Tutorial 3}, with the force
 applied starting at $t = 15\,\text{ps}$. b) Histograms of the dihedral angles of type 2
 in the absence (orange) and in the presence (blue) of the applied force.}
 \label{fig:PEG-distance}