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lammps-tutorials.tex

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@@ -2178,7 +2178,15 @@ \subsubsection{Stretching the PEG molecule}
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Running the \flecmd{pull-with-tip.lmp} file using LAMMPS will generate a trajectory file
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named \flecmd{pull.lammpstrj}, which can be opened in OVITO or VMD.
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Since the trajectory dump file does not contain information about topology and atom types, it is usually preferred to first write out a data file and import it directly (OVITO) or convert it to a PSF file (VMD) and load that before \emph{adding} the trajectory file to it. When using \lammpsgui{} this process can be automated when using \guicmd{View in OVITO} or \guicmd{View in VMD} in the \guicmd{Run} menu. Then only the trajectory dump needs to be added.
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\begin{note}
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Since the trajectory dump file does not contain information about topology and atom
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types, it is usually preferred to first write out a data file and import it directly
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(in the case of OVITO) or convert it to a PSF file (for VMD). This allows the topology
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to be loaded before \emph{adding} the
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trajectory file to it. When using \lammpsgui{}, this process can be automated
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through the \guicmd{View in OVITO} or \guicmd{View in VMD} options in the \guicmd{Run} menu.
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Afterward, only the trajectory dump needs to be added.
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\end{note}
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\subsection{Tutorial 4: Nanosheared electrolyte}
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\label{sheared-confined-label}

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