\begin{tikzpicture}
  \begin{axis}[
      xmin=0, xmax=500, ymin=0, ymax=2,
      width=9cm, height=5cm,
      xlabel={time [ns]}, ylabel={RMSD [nm]}]
    \addplot[mark=none,orange] table[comment chars={@,\#}, x index=0, y index=1] {\relativepath co};
    \addlegendentry{CO}
    \addplot[mark=none,green] table[comment chars={@,\#}, x index=0, y index=1] {\relativepath popc};
    \addlegendentry{POPC}
    \addplot[mark=none,magenta] table[comment chars={@,\#}, x index=0, y index=1] {\relativepath protein};
    \addlegendentry{apoA-I}
  \end{axis}
\end{tikzpicture}