@@ -1918,12 +1918,11 @@ \subsubsection{Breakable bonds}
19181918fix break all bond/break 1000 1 2.5
19191919fix form all bond/create/angle 1000 1 1 2.0 1 aconstrain 90.0 180
19201920\end {lstlisting }
1921-
19221921This `` hack'' works because AIREBO does not pay any attention to bonded
19231922interactions and computes the bond topology dynamically inside the pair
19241923style. Thus adding bonds of bond style \lmpcmd {zero} does not add any
1925- interactions but allow the visualization of them with \lmpcmd {dump
1926- image}. It is, however needed to change the \lmpcmd {special\_ bonds}
1924+ interactions but allows the visualization of them with \lmpcmd {dump
1925+ image}. It is required to change the \lmpcmd {special\_ bonds}
19271926setting to disable any neighbor list exclusions as they are common for
19281927force fields with explicit bonds.
19291928\ begin{lstlisting}
@@ -1949,15 +1948,6 @@ \subsection{Tutorial 3: Polymer in water}
19491948simulations are compared with force spectroscopy experiments, see
19501949Ref.\, ~\citenum {liese2017hydration}.
19511950
1952- \begin {figure }
1953- \centering
1954- \includegraphics [width=0.55\linewidth ]{PEG}
1955- \caption {The polymer molecule (PEG - polyethylene glycol) solvated in water as
1956- simulated during \hyperref [all-atom-label]{Tutorial 3}. Water molecules are
1957- represented as a transparent continuum field for clarity.}
1958- \label {fig:PEG }
1959- \end {figure }
1960-
19611951\begin {note }
19621952{\color {blue}When mixing different force fields, as is done here with GROMOS
19631953and SPC/Fw, users should exercise caution. The choices made in these tutorials
@@ -1969,6 +1959,15 @@ \subsection{Tutorial 3: Polymer in water}
19691959
19701960\subsubsection {Preparing the water reservoir }
19711961
1962+ \begin {figure }
1963+ \centering
1964+ \includegraphics [width=0.55\linewidth ]{PEG}
1965+ \caption {The polymer molecule (PEG - polyethylene glycol) solvated in water as
1966+ simulated during \hyperref [all-atom-label]{Tutorial 3}. Water molecules are
1967+ represented as a transparent continuum field for clarity.}
1968+ \label {fig:PEG }
1969+ \end {figure }
1970+
19721971In this tutorial, the water reservoir is first prepared in the absence of the polymer.
19731972A rectangular box of water is created and equilibrated at ambient temperature and
19741973pressure. The SPC/Fw water model is used~\cite {wu2006flexible }, which is
@@ -2012,7 +2011,7 @@ \subsubsection{Preparing the water reservoir}
20122011 \lmpcmd {special\_ bonds} exclusions are relevant.}
20132012\end {note }
20142013
2015- Let us create a 3D simulation box of dimensions $ 6 \times 3 \times 3 \; \text {nm}^3 $ ,
2014+ \noindent Let us create a 3D simulation box of dimensions $ 6 \times 3 \times 3 \; \text {nm}^3 $ ,
20162015and make space for 8 atom types (2 for the water, 6 for the polymer), 7 bond types
20172016(1 for the water, 6 for the polymer), 8 angle types (1 for the water, 7 for the polymer),
20182017and 4 dihedral types (only for the polymer). Copy the following lines into \flecmd {water.lmp}:
@@ -2044,7 +2043,7 @@ \subsubsection{Preparing the water reservoir}
20442043 maps are used for the bond types, angle types, and dihedral types.
20452044\end {note }
20462045
2047- Let us create water molecules. To do so, let us import a molecule template called
2046+ \noindent Let us create water molecules. To do so, let us import a molecule template called
20482047\flecmd {water.mol} and then randomly create 700 molecules. Add the following
20492048lines into \flecmd {water.lmp}:
20502049\ begin{lstlisting}
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