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move figure to other column to avoid large blocks of whitespace
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lammps-tutorials.tex

Lines changed: 13 additions & 14 deletions
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@@ -1918,12 +1918,11 @@ \subsubsection{Breakable bonds}
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fix break all bond/break 1000 1 2.5
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fix form all bond/create/angle 1000 1 1 2.0 1 aconstrain 90.0 180
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\end{lstlisting}
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This ``hack'' works because AIREBO does not pay any attention to bonded
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interactions and computes the bond topology dynamically inside the pair
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style. Thus adding bonds of bond style \lmpcmd{zero} does not add any
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interactions but allow the visualization of them with \lmpcmd{dump
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image}. It is, however needed to change the \lmpcmd{special\_bonds}
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interactions but allows the visualization of them with \lmpcmd{dump
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image}. It is required to change the \lmpcmd{special\_bonds}
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setting to disable any neighbor list exclusions as they are common for
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force fields with explicit bonds.
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\begin{lstlisting}
@@ -1949,15 +1948,6 @@ \subsection{Tutorial 3: Polymer in water}
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simulations are compared with force spectroscopy experiments, see
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Ref.\,~\citenum{liese2017hydration}.
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\begin{figure}
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\centering
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\includegraphics[width=0.55\linewidth]{PEG}
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\caption{The polymer molecule (PEG - polyethylene glycol) solvated in water as
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simulated during \hyperref[all-atom-label]{Tutorial 3}. Water molecules are
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represented as a transparent continuum field for clarity.}
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\label{fig:PEG}
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\end{figure}
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\begin{note}
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{\color{blue}When mixing different force fields, as is done here with GROMOS
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and SPC/Fw, users should exercise caution. The choices made in these tutorials
@@ -1969,6 +1959,15 @@ \subsection{Tutorial 3: Polymer in water}
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\subsubsection{Preparing the water reservoir}
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\begin{figure}
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\centering
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\includegraphics[width=0.55\linewidth]{PEG}
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\caption{The polymer molecule (PEG - polyethylene glycol) solvated in water as
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simulated during \hyperref[all-atom-label]{Tutorial 3}. Water molecules are
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represented as a transparent continuum field for clarity.}
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\label{fig:PEG}
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\end{figure}
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In this tutorial, the water reservoir is first prepared in the absence of the polymer.
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A rectangular box of water is created and equilibrated at ambient temperature and
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pressure. The SPC/Fw water model is used~\cite{wu2006flexible}, which is
@@ -2012,7 +2011,7 @@ \subsubsection{Preparing the water reservoir}
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\lmpcmd{special\_bonds} exclusions are relevant.}
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\end{note}
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Let us create a 3D simulation box of dimensions $6 \times 3 \times 3 \; \text{nm}^3$,
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\noindent Let us create a 3D simulation box of dimensions $6 \times 3 \times 3 \; \text{nm}^3$,
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and make space for 8 atom types (2 for the water, 6 for the polymer), 7 bond types
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(1 for the water, 6 for the polymer), 8 angle types (1 for the water, 7 for the polymer),
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and 4 dihedral types (only for the polymer). Copy the following lines into \flecmd{water.lmp}:
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maps are used for the bond types, angle types, and dihedral types.
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\end{note}
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Let us create water molecules. To do so, let us import a molecule template called
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\noindent Let us create water molecules. To do so, let us import a molecule template called
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\flecmd{water.mol} and then randomly create 700 molecules. Add the following
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lines into \flecmd{water.lmp}:
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\begin{lstlisting}

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