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Getting Started

If you downloaded the tutorial from the web, the files that you will be needing can be found in a directory called topology-tutorial-files. If you received the files through a workshop, they can be found in the same directory under the path $\sim$/Workshop/topology-tutorial.

This will place you in the directory containing all the necessary files. In the figure below, you can see the structure of this directory.

Figure 1: Directory Structure for tutorial excercises. Output for all simulations is provided in an ``example-output'' subdirectory within each folder shown.
\begin{figure}\begin{center}
\par
\par
\latex{
\includegraphics[scale=0.5]{pictures/directory-structure}
}
\end{center}
\end{figure}

In this section you will learn about typical situations in which you may need to create your own topology file for a given protein or biological molecule. You will learn about biological systems which utilize amino acids other than the ``naturally occurring" 20 and how you may simply be able to alter topology file entries to account for non-standard amino acids without needing to do any new parameterization.


next up previous
Next: Examining the Topology File Up: Topology Tutorial Previous: Required Programs
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