\documentclass[border=10pt]{standalone}
\usepackage{pgfplots, amsmath, pgfplotstable}
\usepackage{filecontents}
\usepgfplotslibrary{colorbrewer}
\usepgfplotslibrary{fillbetween}
\definecolor{color1}{rgb}{0,0,0}
\definecolor{color2}{rgb}{0.5,0.5,0.5}
\definecolor{color3}{rgb}{0.5,0.5,0.5}


\pgfplotsset{every axis plot/.append style={line width=1pt},compat=1.8}

\begin{document}
\begin{tikzpicture}
\begin{axis}[
ylabel=${\rm max}(c)$,
xlabel= $t$,
width = 6cm,
height = 3cm,
%cycle list/Paired-5,
cycle list name=Paired-5,
minor tick style={draw=none}
ymin=0,
]

\addplot+[mark = none, smooth, thick] table[x index=0,y index=1] {Tunnel.txt};
\addplot+[mark = none, smooth, thick] table[x index=0,y index=1] {PartialTunnel.txt};
\end{axis}
\end{tikzpicture}
\\
\begin{tikzpicture}
\begin{axis}[
ylabel=${\rm max}(\varrho_{a})$,
xlabel= $t$,
width = 6cm,
height = 3cm,
%cycle list/Paired-5,
cycle list name=Paired-5,
minor tick style={draw=none}
ymin=0,
]

\addplot+[mark = none, smooth, each nth point=6, thick] table[x index=0,y index=2] {Tunnel.txt};
\addplot+[mark = none, smooth, thick] table[x index=0,y index=2] {PartialTunnel.txt};
\end{axis}
\end{tikzpicture}
\\
\begin{tikzpicture}
\begin{axis}[
ylabel=$x_p$,
xlabel= $t$,
width = 6cm,
height = 3cm,
%cycle list/Paired-5,
cycle list name=Paired-5,
minor tick style={draw=none}
ymin=0,
]

\addplot+[mark = none, smooth, each nth point=6, thick] table[x index=0,y index=3] {Tunnel.txt};
\addplot+[mark = none, smooth, each nth point=6, thick] table[x index=0,y index=3] {PartialTunnel.txt};
\end{axis}
\end{tikzpicture}

\end{document}